The DOI matches its Crossref record; 68 of the 68 references it cites were found in a registry or an index.
A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment
Open accessAbstract
While the roles of parenchymal microglia in brain homeostasis and disease are fairly clear, other brain-resident myeloid cells remain less well understood. By dissecting border regions and combining single-cell RNA-sequencing with high-dimensional cytometry, bulk RNA-sequencing, fate-mapping and microscopy, we reveal the diversity of non-parenchymal brain macrophages. Border-associated macrophages (BAMs) residing in the dura mater, subdural meninges and choroid plexus consisted of distinct subsets with tissue-specific transcriptional signatures, and their cellular composition changed during postnatal development. BAMs exhibited a mixed ontogeny, and subsets displayed distinct self-renewal capacity following depletion and repopulation. Single-cell and fate-mapping analysis both suggested that there is a unique microglial subset residing on the apical surface of the choroid plexus epithelium. Finally, gene network analysis and conditional deletion revealed IRF8 as a master regulator that drives the maturation and diversity of brain macrophages. Our results provide a framework for understanding host-macrophage interactions in both the healthy and diseased brain.
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“Our consensus exAM signature does overlap with the dissociation signature in the study by Van Hove et al.[43] (19 of 25 genes in consensus exAM list; Supplementary Tables 4, 5 and 21a).”
From Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain (2022) · cites this paper as Van Hove et al.[43]
In the citing paper
“Consistent with the reports from other tissues in mice, we found that typical enzymatic digestion of mouse brain tissue induced a host of transcriptional alterations34,43,44,65.”
From Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain (2022) · cites this paper as [43]
In the citing paper
“However, emerging results from other tissues/cell types have begun to characterize dissociation artifacts following enzymatic digestion43–45,65,66.”
From Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain (2022) · cites this paper as [43]
In the citing paper
“No explicit statistical methods were used to predetermine sample sizes but our sample sizes exceed those reported in previous publications32,34,43.”
From Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain (2022) · cites this paper as [43]
In the citing paper
“This molecule likely also affects BAMs, as reported in the case of PLX3397 [317], placing an important caveat on the interpretation of data where PLX5622 is assumed to be purely microglia-specific.”
From Microglia and monocytes in inflammatory CNS disease: integrating phenotype and function (2022) · cites this paper as [317]
In the citing paper
“Although microglia represent a heterogeneous cell population [46], they still share several expression profiles with primitive and adult macrophages, including IBA1.”
From The Cuprizone Model: Dos and Do Nots (2020) · cites this paper as [46]
In the citing paper
“In the Aging Mouse Brain Single Cell Portal, Plcg2 expression is highest in microglia and brain macrophages, with lower levels in endothelial cells and oligodendrocyte precursor cells and minimal to no expression in neurons, astrocytes, and mature oligodendrocytes [30, 72–74].”
From PLCγ2 deficiency compromises systemic immune tolerance and erodes myelin homeostasis while enhancing oxidative metabolism in the mouse brain (2026) · cites this paper as [74]
In the citing paper
“In the Brain Immune Atlas aggregate of CD45+ cells from brain and meningeal regions, Plcg2 transcripts are detected in 18% of immune cells across parenchymal microglia and multiple border-associated macrophage (BAM) subsets, with choroid plexus surface and dural BAMs contributing many Plcg2+ cells and a small B-cell cluster displaying the highest per-cell Plcg2 expression in the dataset [74].”
From PLCγ2 deficiency compromises systemic immune tolerance and erodes myelin homeostasis while enhancing oxidative metabolism in the mouse brain (2026) · cites this paper as [74]
In the citing paper
“We identified a classical monocyte cluster that highly express Ly6c2, and a non-classical monocyte cluster highly express Itgal, similarly as a published single cell RNA-seq study.88”
From TET2-mutant myeloid cells mitigate Alzheimer’s disease progression via CNS infiltration and enhanced phagocytosis in mice (2025) · cites this paper as [88]
In the citing paper
“In addition, we confirmed previous findings of elevated expression of lipid-related genes in BAMs (31) and observed an increase in LD content within these cells over time and during disease progression.”
From Reducing microglial lipid load enhances β amyloid phagocytosis in an Alzheimer’s disease mouse model (2025) · cites this paper as [31]
In the citing paper
“MHCII+ macrophages are most abundant in the choroid plexus and meninges [37], and we similarly observe widespread uptake of L2-siRNA in this population (Fig. 5F).”
From Elucidating brain transport pathways and cell type-dependent gene silencing of a durable lipid–siRNA conjugate administered into cerebrospinal fluid (2025) · cites this paper as [37]
In the citing paper
“MHCII+ macrophages are most abundant in the choroid plexus and meninges,43 and we similarly observe widespread uptake of L2-siRNA in this population (Fig. 5F).”
From Lipid-siRNA conjugate accesses a perivascular transport mechanism and achieves widespread and durable knockdown in the central nervous system (2024) · cites this paper as [43]
In the citing paper
“The yolk sac-derived precursors of resident macrophages are only in the perivascular compartment [360,361], where they maintain their cellular origin in adulthood [362,363,364].”
From Revisiting the Pathogenesis of X-Linked Adrenoleukodystrophy (2025) · cites this paper as [364]
In the citing paper
“As immune surveillants, CAMs clear harmful substances through phagocytosis, antigen presentation, and cytokine production [364,368,371,372,373,374,375,376]”
From Revisiting the Pathogenesis of X-Linked Adrenoleukodystrophy (2025) · cites this paper as [364]
In the citing paper
“CD38 expression was associated with neuroinflammation with greater amounts of proinflammatory macrophages/microglia in mouse brains160,165.”
From NAD+ metabolism and its roles in cellular processes during ageing (2021) · cites this paper as [165]
In the citing paper
“This contrasts with macrophages in the choroid plexus and dura mater, which do turn over and receive some input from peripheral blood monocytes during adulthood (71-73).”
From The anatomy and immunology of vasculature in the central nervous system (2019) · cites this paper as [73]
In the citing paper
“Like microglia, most macrophages residing in the leptomeninges and perivascular spaces are derived from early yolk sac–derived erythromyeloid progenitors, and during steady state, these cells have minimal turnover.”
From The anatomy and immunology of vasculature in the central nervous system (2019) · cites this paper as [73]
In the citing paper
“On the basis of high-parameter mass cytometry and single-cell RNA-sequencing studies, the dural macrophages appear to be distinct from those residing in the pia and underlying parenchyma (73, 94).”
From The anatomy and immunology of vasculature in the central nervous system (2019) · cites this paper as [73]
In the citing paper
“The macrophages expressed markers of border associated macrophages (BAMs) (e.g., Apoe, Ms4a7, Ms4a6c) recently identified in periluminal regions, meninges, and ChP (Van Hove et al., 2019).”
From A cellular and spatial map of the choroid plexus across brain ventricles and ages (2021) · cites this paper as Van Hove et al., 2019
In the citing paper
“Similarly, we found a subset of macrophages expressing markers previously defined as subdural-specific BAMs (e.g., Lyve1, Ednrb, Colec12; Van Hove et al., 2019) that were enriched in embryonic ChP macrophages in our dataset (Figure S5H).”
From A cellular and spatial map of the choroid plexus across brain ventricles and ages (2021) · cites this paper as Van Hove et al., 2019
In the citing paper
“However, in contrast to Van Hove et al., our data revealed that this separation was age-dependent and potentially represented a maturation-dependent shift from MHC IIlow to MHC IIhigh (Figure 5I, S5I,J, Table S6).”
From A cellular and spatial map of the choroid plexus across brain ventricles and ages (2021) · cites this paper as Van Hove et al., 2019
In the citing paper
“In agreement with recent reports (Van Hove et al., 2019), we found diversity within the BAMs, which segregated into two subsets defined as major histocompatibility complex (MHC) class IIlow and MHC IIhigh.”
From A cellular and spatial map of the choroid plexus across brain ventricles and ages (2021) · cites this paper as Van Hove et al., 2019
In the citing paper
“These maturation dependent changes agree with a recent report of BAMs (Van Hove et al., 2019).”
From A cellular and spatial map of the choroid plexus across brain ventricles and ages (2021) · cites this paper as Van Hove et al., 2019
Citations
Cites
Fiji: an open-source platform for biological-image analysis
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829
Near-optimal probabilistic RNA-seq quantification
Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016) · Nature Biotechnology · doi:10.1038/nbt.3519 · Cited by 9,723
Spatial reconstruction of single-cell gene expression data
Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3192 · Cited by 7,055
A robust and high-throughput Cre reporting and characterization system for the whole mouse brain
Madisen, L., Zwingman, T. A., Sunkin, S. M., Oh, S. W., Zariwala, H. A., Gu, H., Ng, L. L., Palmiter, R. D., Hawrylycz, M. J., Jones, A. R., et al. (2010) · Nature Neuroscience · doi:10.1038/nn.2467 · Cited by 6,907
Scenic: single-cell regulatory network inference and clustering.
Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4463 · Cited by 6,520
Self-citationlimma: Linear Models for Microarray Data
Smyth, G. K. (2005) · Statistics for Biology and Health · doi:10.1007/0-387-29362-0_23 · Cited by 5,796
A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease
Keren-Shaul, H., Spinrad, A., Weiner, A., Matcovitch-Natan, O., Dvir-Szternfeld, R., Ulland, T. K., David, E., Baruch, K., Lara-Astaiso, D., Toth, B., et al. (2017) · Cell · doi:10.1016/j.cell.2017.05.018 · Cited by 5,493
Structural and functional features of central nervous system lymphatic vessels
Louveau, A., Smirnov, I., Keyes, T. J., Eccles, J. D., Rouhani, S. J., Peske, J. D., Derecki, N. C., Castle, D., Mandell, J. W., Lee, K. S., et al. (2015) · Nature · doi:10.1038/nature14432 · Cited by 4,413
Cited by
Sorted by citations
Microglia states and nomenclature: A field at its crossroads
Paolicelli, R. C., Sierra, A., Stevens, B., Tremblay, M.-E., Aguzzi, A., Ajami, B., Amit, I., Audinat, E., Bechmann, I., Bennett, M., et al. (2022) · Neuron · doi:10.1016/j.neuron.2022.10.020 · Cited by 1,973
“Thus, although still widely used, ‘‘resting’’ and ‘‘activated’’ microglia are labels that should be discontinued. represent their transcriptional identity and are commonly employed as ‘‘microglial markers’’ (Table 1).”
NAD+ metabolism and its roles in cellular processes during ageing
Covarrubias, A. J., Perrone, R., Grozio, A., & Verdin, E. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-00313-x · Cited by 1,617
Microglia Biology: One Century of Evolving Concepts
Prinz, M., Jung, S., & Priller, J. (2019) · Cell · doi:10.1016/j.cell.2019.08.053 · Cited by 1,525
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Yao, Z., van Velthoven, C. T. J., Kunst, M., Zhang, M., McMillen, D., Lee, C., Jung, W., Goldy, J., Abdelhak, A., Aitken, M., et al. (2023) · Nature · doi:10.1038/s41586-023-06812-z · Cited by 1,203
Signaling inflammation across the gut-brain axis
Agirman, G., Yu, K. B., & Hsiao, E. Y. (2021) · Science · doi:10.1126/science.abi6087 · Cited by 867
Microglia: Immune and non-immune functions
Borst, K., Dumas, A. A., & Prinz, M. (2021) · Immunity · doi:10.1016/j.immuni.2021.09.014 · Cited by 804
Microglia Heterogeneity in the Single-Cell Era
Masuda, T., Sankowski, R., Staszewski, O., & Prinz, M. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.010 · Cited by 784
Pombo Antunes, A. R., Scheyltjens, I., Lodi, F., Messiaen, J., Antoranz, A., Duerinck, J., Kancheva, D., Martens, L., De Vlaminck, K., Van Hove, H., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-020-00789-y · Cited by 704
Self-citationFriebel, E., Kapolou, K., Unger, S., Núñez, N. G., Utz, S. G., Rushing, E. J., Regli, L., Weller, M., Greter, M., Tugues, S., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.055 · Cited by 675
Functional characterization of the dural sinuses as a neuroimmune interface
Rustenhoven, J., Drieu, A., Mamuladze, T., de Lima, K. A., Dykstra, T., Wall, M., Papadopoulos, Z., Kanamori, M., Salvador, A. F., Baker, W., et al. (2021) · Cell · doi:10.1016/j.cell.2020.12.040 · Cited by 685
Skull and vertebral bone marrow are myeloid cell reservoirs for the meninges and CNS parenchyma
Cugurra, A., Mamuladze, T., Rustenhoven, J., Dykstra, T., Beroshvili, G., Greenberg, Z. J., Baker, W., Papadopoulos, Z., Drieu, A., Blackburn, S., et al. (2021) · Science · doi:10.1126/science.abf7844 · Cited by 681
Cross-tissue single-cell landscape of human monocytes and macrophages in health and disease
Mulder, K., Patel, A. A., Kong, W. T., Piot, C., Halitzki, E., Dunsmore, G., Khalilnezhad, S., Irac, S. E., Dubuisson, A., Chevrier, M., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.07.007 · Cited by 678
Tissue-specific macrophages: how they develop and choreograph tissue biology
Mass, E., Nimmerjahn, F., Kierdorf, K., & Schlitzer, A. (2023) · Nature Reviews Immunology · doi:10.1038/s41577-023-00848-y · Cited by 621
Microglia and Central Nervous System–Associated Macrophages—From Origin to Disease Modulation
Prinz, M., Masuda, T., Wheeler, M. A., & Quintana, F. J. (2021) · Annual Review of Immunology · doi:10.1146/annurev-immunol-093019-110159 · Cited by 584
Wang, S., Mustafa, M., Yuede, C. M., Salazar, S. V., Kong, P., Long, H., Ward, M., Siddiqui, O., Paul, R., Gilfillan, S., et al. (2020) · Journal of Experimental Medicine · doi:10.1084/jem.20200785 · Cited by 549
Dick, S. A., Wong, A., Hamidzada, H., Nejat, S., Nechanitzky, R., Vohra, S., Mueller, B., Zaman, R., Kantores, C., Aronoff, L., et al. (2022) · Science Immunology · doi:10.1126/sciimmunol.abf7777 · Cited by 538
Neuroinflammation in Alzheimer disease
Heneka, M. T., van der Flier, W. M., Jessen, F., Hoozemanns, J., Thal, D. R., Boche, D., Brosseron, F., Teunissen, C., Zetterberg, H., Jacobs, A. H., et al. (2025) · Nature Reviews Immunology · doi:10.1038/s41577-024-01104-7 · Cited by 638
“…system (CNS), local macrophages exist in two distinct flavours: either as juxta-neuronal macrophages in the parenchyma — where they are traditionally called microglia — or as resident macrophages at CNS interfaces such as the leptomeninges, the perivascular space and choroid plexus 210–212 .”
Metabolic modeling of single Th17 cells reveals regulators of autoimmunity
Wagner, A., Wang, C., Fessler, J., DeTomaso, D., Avila-Pacheco, J., Kaminski, J., Zaghouani, S., Christian, E., Thakore, P., Schellhaass, B., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.045 · Cited by 524
What is a cell type and how to define it?
Zeng, H. (2022) · Cell · doi:10.1016/j.cell.2022.06.031 · Cited by 439
Single-cell RNA sequencing reveals functional heterogeneity of glioma-associated brain macrophages
Ochocka, N., Segit, P., Walentynowicz, K. A., Wojnicki, K., Cyranowski, S., Swatler, J., Mieczkowski, J., & Kaminska, B. (2021) · Nature Communications · doi:10.1038/s41467-021-21407-w · Cited by 484
Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders
Brioschi, S., Wang, W.-L., Peng, V., Wang, M., Shchukina, I., Greenberg, Z. J., Bando, J. K., Jaeger, N., Czepielewski, R. S., Swain, A., et al. (2021) · Science · doi:10.1126/science.abf9277 · Cited by 472
White matter aging drives microglial diversity
Safaiyan, S., Besson-Girard, S., Kaya, T., Cantuti-Castelvetri, L., Liu, L., Ji, H., Schifferer, M., Gouna, G., Usifo, F., Kannaiyan, N., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.01.027 · Cited by 477
Mapping microglia states in the human brain through the integration of high-dimensional techniques
Sankowski, R., Böttcher, C., Masuda, T., Geirsdottir, L., Sagar, Sindram, E., Seredenina, T., Muhs, A., Scheiwe, C., Shah, M. J., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0532-y · Cited by 449
Marsh, S. E., Walker, A. J., Kamath, T., Dissing-Olesen, L., Hammond, T. R., de Soysa, T. Y., Young, A. M. H., Murphy, S., Abdulraouf, A., Nadaf, N., et al. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01022-8 · Cited by 431
Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development
Utz, S. G., See, P., Mildenberger, W., Thion, M. S., Silvin, A., Lutz, M., Ingelfinger, F., Rayan, N. A., Lelios, I., Buttgereit, A., et al. (2020) · Cell · doi:10.1016/j.cell.2020.03.021 · Cited by 436
Marsh, S. E., Kamath, T., Walker, A. J., Dissing-Olesen, L., Hammond, T. R., Young, A. M. H., Abdulraouf, A., Nadaf, N., Dufort, C., Murphy, S., et al. (2020) · doi:10.1101/2020.12.03.408542 · Cited by 430
Macrophages and microglia in glioblastoma: heterogeneity, plasticity, and therapy
Khan, F., Pang, L., Dunterman, M., Lesniak, M. S., Heimberger, A. B., & Chen, P. (2023) · Journal of Clinical Investigation · doi:10.1172/jci163446 · Cited by 431
Meningeal γδ T cells regulate anxiety-like behavior via IL-17a signaling in neurons
Alves de Lima, K., Rustenhoven, J., Da Mesquita, S., Wall, M., Salvador, A. F., Smirnov, I., Martelossi Cebinelli, G., Mamuladze, T., Baker, W., Papadopoulos, Z., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0776-4 · Cited by 416
Macrophages at CNS interfaces: Ontogeny and function in health and disease
Kierdorf, K., Masuda, T., Jordão, M. J. C., & Prinz, M. (2019) · Nature Reviews Neuroscience · doi:10.1038/s41583-019-0201-x · Cited by 416
Neuromodulation by the immune system: a focus on cytokines
Salvador, A. F., de Lima, K. A., & Kipnis, J. (2021) · Nature Reviews Immunology · doi:10.1038/s41577-021-00508-z · Cited by 389
Immune cell regulation of glia during CNS injury and disease
Greenhalgh, A. D., David, S., & Bennett, F. C. (2020) · Nature reviews. Neuroscience · doi:10.1038/s41583-020-0263-9 · Cited by 411
Rojo, R., Raper, A., Ozdemir, D. D., Lefèvre, L., Grabert, K., Wollscheid-Lengeling, E., Bradford, B. M., Caruso, M., Gažová, I., Sánchez, A., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11053-8 · Cited by 390
A cellular and spatial map of the choroid plexus across brain ventricles and ages
Dani, N., Herbst, R. H., McCabe, C., Green, G. S., Kaiser, K., Head, J. P., Cui, J., Shipley, F. B., Jang, A., Dionne, D., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.003 · Cited by 388
Tissue macrophages: origin, heterogenity, biological functions, diseases and therapeutic targets
Guan, F., Wang, R., Yi, Z., Luo, P., Liu, W., Xie, Y., Liu, Z., Xia, Z., Zhang, H., & Cheng, Q. (2025) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-025-02124-y · Cited by 371
Silvin, A., Uderhardt, S., Piot, C., Da Mesquita, S., Yang, K., Geirsdottir, L., Mulder, K., Eyal, D., Liu, Z., Bridlance, C., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.07.004 · Cited by 368
Alves de Lima, K., Rustenhoven, J., & Kipnis, J. (2020) · Annual Review of Immunology · doi:10.1146/annurev-immunol-102319-103410 · Cited by 348
Hu, Y., Fryatt, G. L., Ghorbani, M., Obst, J., Menassa, D. A., Martin-Estebane, M., Muntslag, T. A. O., Olmos-Alonso, A., Guerrero-Carrasco, M., Thomas, D., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109228 · Cited by 298
The anatomy and immunology of vasculature in the central nervous system
Mastorakos, P., & McGavern, D. (2019) · Science Immunology · doi:10.1126/sciimmunol.aav0492 · Cited by 333
GABA-Receptive Microglia Selectively Sculpt Developing Inhibitory Circuits
Favuzzi, E., Huang, S., Saldi, G.-A., Binan, L., Ibrahim, L. A., Fernández-Otero, M., Cao, Y., Zeine, A., Sefah, A., Zheng, K., et al. (2020) · Cell · doi:10.1016/j.cell.2021.06.018 · Cited by 327
“The almost complete absence of cells expressing Ms4a7 confirmed that CNS border-associated macrophages (BAMs) (Van Hove et al., 2019) were not contaminating the dataset.”
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Kinuthia, U. M., Wolf, A., & Langmann, T. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.564077 · Cited by 332
Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease
Piwecka, M., Rajewsky, N., & Rybak-Wolf, A. (2023) · Nature Reviews Neurology · doi:10.1038/s41582-023-00809-y · Cited by 320
Parenchymal border macrophages regulate the flow dynamics of the cerebrospinal fluid
Drieu, A., Du, S., Storck, S. E., Rustenhoven, J., Papadopoulos, Z., Dykstra, T., Zhong, F., Kim, K., Blackburn, S., Mamuladze, T., et al. (2022) · Nature · doi:10.1038/s41586-022-05397-3 · Cited by 325
Novel Hexb-based tools for studying microglia in the CNS
Masuda, T., Amann, L., Sankowski, R., Staszewski, O., Lenz, M., d´Errico, P., Snaidero, N., Costa Jordão, M. J., Böttcher, C., Kierdorf, K., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0707-4 · Cited by 317
Leo, A. D., Ugolini, A., Yu, X., Scirocchi, F., Scocozza, D., Peixoto, B., Pace, A., D’Angelo, L., Liu, J. K., Etame, A. B., et al. (2024) · Immunity · doi:10.1016/j.immuni.2024.04.006 · Cited by 348
Macrophage spatial heterogeneity in gastric cancer defined by multiplex immunohistochemistry
Huang, Y., Wang, M., Yu, S. Y., Costanzo, N. D., Mitchell, C., Achuthan, A. A., Hamilton, J. A., Busuttil, R. A., & Boussioutas, A. (2019) · Nature Communications · doi:10.1038/s41467-019-11788-4 · Cited by 301
Microglia coordinate cellular interactions during spinal cord repair in mice
Brennan, F. H., Li, Y., Wang, C., Ma, A., Guo, Q., Li, Y., Pukos, N., Campbell, W. A., Witcher, K. G., Guan, Z., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31797-0 · Cited by 323
Osorio, D., Zhong, Y., Li, G., Xu, Q., Yang, Y., Hillhouse, A., Chen, J., Davidson, L. A., Tian, Y., Chapkin, R. S., et al. (2021) · Patterns · doi:10.1016/j.patter.2022.100434 · Cited by 406
“These microglial cells were derived from WT homeostatic mice.”
MethodSingle-cell RNA-seq reveals the transcriptional landscape in ischemic stroke
Zheng, K., Lin, L., Jiang, W., Chen, L., Zhang, X., Zhang, Q., Ren, Y., & Hao, J. (2021) · Journal of Cerebral Blood Flow & Metabolism · doi:10.1177/0271678x211026770 · Cited by 308
Specification of CNS macrophage subsets occurs postnatally in defined niches
Masuda, T., Amann, L., Monaco, G., Sankowski, R., Staszewski, O., Krueger, M., Del Gaudio, F., He, L., Paterson, N., Nent, E., et al. (2022) · Nature · doi:10.1038/s41586-022-04596-2 · Cited by 294
De Schepper, S., Ge, J. Z., Sierksma, A., Crowley, G., Ferreira, L. S. S., Garceau, D., Toomey, C. E., Sokolova, D., Rueda-Carrasco, J., Shin, S.-H., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01257-z · Cited by 295
“Microglia and PVMs both share similar yolk-sac origin and reside on the parenchymal side of the BBB, yet occupy distinct microenvironments and express unique cell-type-specific markers 8–13 .”
Self-citationSingle-cell RNA sequencing reveals evolution of immune landscape during glioblastoma progression
Yeo, A. T., Rawal, S., Delcuze, B., Christofides, A., Atayde, A. M. P., Strauss, L., Balaj, L., Rogers, V. A., Uhlmann, E. J., Varma, H., et al. (2022) · Nature Immunology · doi:10.1038/s41590-022-01215-0 · Cited by 303
A human circulating immune cell landscape in aging and COVID-19
Zheng, Y., Liu, X., Le, W., Xie, L., Li, H., Wen, W., Wang, S., Ma, S., Huang, Z., Ye, J., et al. (2020) · Protein & Cell · doi:10.1007/s13238-020-00762-2 · Cited by 270
Single-cell analysis of the cellular heterogeneity and interactions in the injured mouse spinal cord
Milich, L. M., Choi, J. S., Ryan, C. B., Cerqueira, S. R., Benavides, S., Yahn, S. L., Tsoulfas, P., & Lee, J. K. (2021) · The Journal of Experimental Medicine · doi:10.1084/jem.20210040 · Cited by 289
Antunes, A. R. P., Scheyltjens, I., Duerinck, J., Neyns, B., Movahedi, K., & Ginderachter, J. A. V. (2020) · eLife · doi:10.7554/elife.52176 · Cited by 279
Self-citationLipid and Lipoprotein Metabolism in Microglia
Loving, B. A., & Bruce, K. D. (2020) · Frontiers in Physiology · doi:10.3389/fphys.2020.00393 · Cited by 255
Dynamics of Cardiac Neutrophil Diversity in Murine Myocardial Infarction
Vafadarnejad, E., Rizzo, G., Krampert, L., Arampatzi, P., Arias-Loza, P.-A., Nazzal, Y., Rizakou, A., Knochenhauer, T., Bandi, S. R., Nugroho, V. A., et al. (2020) · Circulation Research · doi:10.1161/circresaha.120.317200 · Cited by 268
Cerebrospinal fluid regulates skull bone marrow niches via direct access through dural channels
Mazzitelli, J. A., Smyth, L. C. D., Cross, K. A., Dykstra, T., Sun, J., Du, S., Mamuladze, T., Smirnov, I., Rustenhoven, J., & Kipnis, J. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01029-1 · Cited by 261
Brain borders at the central stage of neuroimmunology
Rustenhoven, J., & Kipnis, J. (2022) · Nature · doi:10.1038/s41586-022-05474-7 · Cited by 253
Macrophages and microglia: the cerberus of glioblastoma
Buonfiglioli, A., & Hambardzumyan, D. (2021) · Acta Neuropathologica Communications · doi:10.1186/s40478-021-01156-z · Cited by 254
“BAMs are also present in the choroid plexus, where they are further classified as stromal macrophages and Kolmer’s epiplexus cells, whose ontogeny is more complex: both have been shown to originate during embryogenesis from EMPs, but only the former present high self-renewal from BM monocytes postnatally [25].”
BackgroundYdens, E., Amann, L., Asselbergh, B., Scott, C. L., Martens, L., Sichien, D., Mossad, O., Blank, T., Prijck, S. D., Low, D., et al. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0618-6 · Cited by 251
Self-citationMei, Y., Wang, X., Zhang, J., Liu, D., He, J., Huang, C., Liao, J., Wang, Y., Feng, Y.-Y., Li, H., et al. (2023) · Nature Cancer · doi:10.1038/s43018-023-00598-9 · Cited by 232
Microenvironmental Regulation of Tumor Progression and Therapeutic Response in Brain Metastasis
Schulz, M., Salamero‐Boix, A., Niesel, K., Alekseeva, T., & Sevenich, L. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01713 · Cited by 226
Microglia and monocytes in inflammatory CNS disease: integrating phenotype and function
Spiteri, A. G., Wishart, C. L., Pamphlett, R., Locatelli, G., & King, N. J. C. (2022) · Acta Neuropathologica · doi:10.1007/s00401-021-02384-2 · Cited by 216
“In the healthy homeostatic CNS, microglia comprise the predominant myeloid population, followed by nonparenchymal CNS macrophages [182], collectively called CNS- or border-associated macrophages (CAMs or BAMs) [20, 235, 259].”
BackgroundInfluentialBacteria hijack a meningeal neuroimmune axis to facilitate brain invasion
Pinho-Ribeiro, F. A., Deng, L., Neel, D. V., Erdoğan, Ö., Basu, H., Yang, D., Choi, S., Walker, A. J., Carneiro-Nascimento, S., He, K., et al. (2023) · Nature · doi:10.1038/s41586-023-05753-x · Cited by 219
Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation
Mendiola, A. S., Ryu, J. K., Bardehle, S., Meyer-Franke, A., Ang, K. K.-H., Wilson, C., Baeten, K. M., Hanspers, K., Merlini, M., Thomas, S., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0654-0 · Cited by 199
CXCR6 orchestrates brain CD8+ T cell residency and limits mouse Alzheimer’s disease pathology
Su, W., Saravia, J., Risch, I., Rankin, S. L., Guy, C. S., Chapman, N. M., Shi, H., Sun, Y., Anil, K. C., Li, W., et al. (2023) · Nature Immunology · doi:10.1038/s41590-023-01604-z · Cited by 222
“FASTQ files from 16-month-old APP/PS1 and Non-Tg mice 11 (PRJNA529095) were downloaded.”
BackgroundVan Damme, H., Dombrecht, B., Kiss, M., Roose, H., Allen, E., Van Overmeire, E., Kancheva, D., Martens, L., Murgaski, A., Bardet, P. M. R., et al. (2021) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-001749 · Cited by 205
“30 The obtained clustering was visualized in two-dimensional scatter plots via Uniform Manifold Approximation and Projection (UMAP) using the Seurat V3.”
Self-citationEmergence and Developmental Roles of the Cerebrospinal Fluid System
Fame, R. M., & Lehtinen, M. K. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.01.027 · Cited by 211
Phagocytic microglia and macrophages in brain injury and repair
Yu, F., Wang, Y., Stetler, R. A., Leak, R. K., Hu, X., & Chen, J. (2022) · CNS Neuroscience & Therapeutics · doi:10.1111/cns.13899 · Cited by 213
Autophagy enables microglia to engage amyloid plaques and prevents microglial senescence
Choi, I., Wang, M., Yoo, S., Xu, P., Seegobin, S. P., Li, X., Han, X., Wang, Q., Peng, J., Zhang, B., et al. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01158-0 · Cited by 202
APOE4 impairs the microglial response in Alzheimer’s disease by inducing TGFβ-mediated checkpoints
Yin, Z., Rosenzweig, N., Kleemann, K. L., Zhang, X., Brandão, W., Margeta, M. A., Schroeder, C., Sivanathan, K. N., Silveira, S., Gauthier, C., et al. (2023) · Nature Immunology · doi:10.1038/s41590-023-01627-6 · Cited by 202
“To distinguish peripheral recruited myeloid cells and BAMs from microglia, we reclustered all microglia-like cells and identified Ms4a7 + and Mrc1 + macrophages 25,26 and Lyve1 + BAMs 27,28 (Extended Data Fig.”
BackgroundGarcía‐Bonilla, L., Shahanoor, Z., Sciortino, R. K., Nazarzoda, O., Racchumi, G., Iadecola, C., & Anrather, J. (2024) · Nature Immunology · doi:10.1038/s41590-023-01711-x · Cited by 225
Intersection of pathological tau and microglia at the synapse
Vogels, T., Murgoci, A.-N., & Hromádka, T. (2019) · Acta Neuropathologica Communications · doi:10.1186/s40478-019-0754-y · Cited by 197
Zernecke, A., Erhard, F., Weinberger, T., Schulz, C., Ley, K. F., Saliba, A., & Cochain, C. (2022) · Cardiovascular Research · doi:10.1093/cvr/cvac161 · Cited by 214
Wei, J., Chen, P., Gupta, P., Ott, M., Zamler, D. B., Kassab, C., Bhat, K., Curran, M. A., de Groot, J., & Heimberger, A. B. (2019) · Neuro-Oncology · doi:10.1093/neuonc/noz212 · Cited by 192
Emerging roles for CNS fibroblasts in health, injury and disease
Dorrier, C., Jones, H. E., Pintarić, L., Siegenthaler, J. A., & Daneman, R. (2021) · Nature reviews. Neuroscience · doi:10.1038/s41583-021-00525-w · Cited by 204
Conserved meningeal lymphatic drainage circuits in mice and humans
Jacob, L., Brito, J. M., Lenck, S., Corcy, C., Benbelkacem, F., Geraldo, L. H., Xu, Y., Thomas, J.-M., Kamouh, M.-R. E., Spajer, M., et al. (2022) · The Journal of Experimental Medicine · doi:10.1084/jem.20220035 · Cited by 206
Schafflick, D., Wolbert, J., Heming, M., Thomas, C., Hartlehnert, M., Börsch, A., Ricci, A., Martín-Salamanca, S., Li, X., Lu, I., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-021-00880-y · Cited by 188
Distinct molecular profiles of skull bone marrow in health and neurological disorders
Kolabas, Z. I., Kuemmerle, L. B., Perneczky, R., Förstera, B., Ulukaya, S., Ali, M., Kapoor, S., Bartos, L. M., Büttner, M., Çalışkan, Ö. Ş., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.009 · Cited by 196
Boeck, A. D., Ahn, B. Y., D’Mello, C., Lun, X. Q., Menon, S. V., Alshehri, M. M., Szulzewsky, F., Shen, Y., Khan, L., Dang, N. H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18569-4 · Cited by 191
Astrocytic phagocytosis is a compensatory mechanism for microglial dysfunction
Konishi, H., Okamoto, T., Hara, Y., Komine, O., Tamada, H., Maeda, M., Osako, F., Kobayashi, M., Nishiyama, A., Kataoka, Y., et al. (2020) · The EMBO Journal · doi:10.15252/embj.2020104464 · Cited by 179
“…(Fig EV2D and E), indicating that survived microglia actively proliferate to replenish the brain, which is similar to other microglial ablation models, such as using Cx3cr1 CreER : Rosa26 dtr mice (Bruttger et al , 2015) or CSF1R inhibitor PLX compounds (Huang et al , 2018; Van Hove et al , 2019).”
InfluentialShemer, A., Scheyltjens, I., Frumer, G. R., Kim, J.-S., Grozovski, J., Ayanaw, S., Dassa, B., Van Hove, H., Chappell-Maor, L., Boura-Halfon, S., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.09.018 · Cited by 175
Self-citationTansley, S. N., Uttam, S., Guzmán, A. U., Yaqubi, M., Pacis, A., Parisien, M., Deamond, H., Wong, C., Rabau, O., Brown, N., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28473-8 · Cited by 194
A Binary Cre Transgenic Approach Dissects Microglia and CNS Border-Associated Macrophages
Kim, J.-S., Kolesnikov, M., Peled-Hajaj, S., Scheyltjens, I., Xia, Y., Trzebanski, S., Haimon, Z., Shemer, A., Lubart, A., Van Hove, H., et al. (2021) · Immunity · doi:10.1016/j.immuni.2020.11.007 · Cited by 176
Self-citationA new genetic strategy for targeting microglia in development and disease
McKinsey, G. L., Lizama, C. O., Keown-Lang, A. E., Niu, A., Santander, N., Larpthaveesarp, A., Chee, E., Gonzalez, F. F., & Arnold, T. D. (2020) · eLife · doi:10.7554/elife.54590 · Cited by 176
Glioblastoma heterogeneity at single cell resolution
Eisenbarth, D., & Wang, Y. (2023) · Oncogene · doi:10.1038/s41388-023-02738-y · Cited by 179
“Microglia can be identified by the expression of genes, such as TMEM119, P2RY12, and CX3CR1 but can exhibit significant differences in gene expression profiles depending on underlying mutations or progression status [57, 58].”
BackgroundInfluentialTissue-resident macrophages: guardians of organ homeostasis
Nobs, S. P., & Köpf, M. (2021) · Trends in Immunology · doi:10.1016/j.it.2021.04.007 · Cited by 180
The Cuprizone Model: Dos and Do Nots
Zhan, J., Mann, T., Joost, S., Behrangi, N., Frank, M., & Kipp, M. (2020) · Cells · doi:10.3390/cells9040843 · Cited by 171
“Although microglia represent a heterogeneous cell population [46], they still share several expression profiles with primitive and adult macrophages, including IBA1.”
BackgroundMicroglia versus Monocytes: Distinct Roles in Degenerative Diseases of the Retina
Chen, Y., Roubeix, C., Sennlaub, F., & Saban, D. R. (2020) · Trends in Neurosciences · doi:10.1016/j.tins.2020.03.012 · Cited by 169
“Another example of microgliarestricted access might also be gleaned in the normal mouse brain, where a distinctive microglial population, but not the choroid plexus macrophage population, was found to reside on the apical epithelium of the choroid plexus [93].”
BackgroundVlaminck, K. D., Hove, H. V., Kancheva, D., Scheyltjens, I., Antunes, A. R. P., Bastos, J., Vara‐Pérez, M., Ali, L., Mampay, M., Deneyer, L., et al. (2021) · Immunity · doi:10.1016/j.immuni.2022.09.005 · Cited by 169
Self-citationFunction of Macrophages in Disease: Current Understanding on Molecular Mechanisms
Zhang, C., Yang, M. J., & Ericsson, A. C. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.620510 · Cited by 181
Wang, P. L., Yim, A. K., Kim, K.-W., Avey, D. R., Czepielewski, R. S., Colonna, M., Milbrandt, J., Randolph, G. J., & The Immunological Genome Project (2020) · Nature Communications · doi:10.1038/s41467-020-16355-w · Cited by 168
When encephalitogenic T cells collaborate with microglia in multiple sclerosis
Dong, Y., & Yong, V. W. (2019) · Nature Reviews Neurology · doi:10.1038/s41582-019-0253-6 · Cited by 169
Schonhoff, A. M., Figge, D. A., Williams, G. P., Jurkuvenaite, A., Gallups, N. J., Childers, G. M., Webster, J. M., Standaert, D. G., Goldman, J. E., & Harms, A. S. (2023) · Nature Communications · doi:10.1038/s41467-023-39060-w · Cited by 161
“48 hours apart, as previously described [11, 29].”
Multiomic spatial landscape of innate immune cells at human central nervous system borders
Sankowski, R., Süß, P., Benkendorff, A., Böttcher, C., Fernandez-Zapata, C., Chhatbar, C., Cahueau, J., Monaco, G., Gasull, A. D., Khavaran, A., et al. (2024) · Nature Medicine · doi:10.1038/s41591-023-02673-1 · Cited by 156
“Divergently regulated genes macrophages represent the main immune cells at CNS interfaces 8,9 .”
BackgroundMethodInfluentialIadecola, C., Smith, E. E., Anrather, J., Gu, C., Mishra, A., Misra, S., Pérez‐Pinzón, M. A., Shih, A. Y., Sorond, F. A., van Veluw, S. J., et al. (2023) · Stroke · doi:10.1161/str.0000000000000431 · Cited by 161
Pro-inflammatory and proliferative microglia drive progression of glioblastoma
Liu, H., Sun, Y., Zhang, Q., Jin, W., Gordon, R. E., Zhang, Y., Wang, J., Sun, C., Wang, Z., Qi, X., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109718 · Cited by 144
Insights into Alzheimer’s disease from single-cell genomic approaches
Murdock, M. H., & Tsai, L.-H. (2023) · Nature Neuroscience · doi:10.1038/s41593-022-01222-2 · Cited by 148
The choroid plexus links innate immunity to CSF dysregulation in hydrocephalus
Robert, S. M., Reeves, B. C., Kiziltug, E., Duy, P. Q., Karimy, J. K., Mansuri, M. S., Marlier, A., Allington, G., Greenberg, A. B. W., DeSpenza, T., et al. (2023) · Cell · doi:10.1016/j.cell.2023.01.017 · Cited by 162
“We next integrated our bulk multi-omics ChP data with published single-cell and single-nucleus RNA-seq (sc- and snRNAseq, respectively) of the ChP and brain macrophages.(6,60) We constructed 21 modules of co-expressed genes from a published scRNA-seq dataset of rodent ChP(60) (Figure 2F) and found that PIH-associated…”
MethodResultInfluentialSelf-citationAnalyzing microglial phenotypes across neuropathologies: a practical guide
Schwabenland, M., Brück, W., Priller, J., Stadelmann, C., Lassmann, H., & Prinz, M. (2021) · Acta Neuropathologica · doi:10.1007/s00401-021-02370-8 · Cited by 149
Metadata
- Authors
- Van Hove, H., Martens, L., Scheyltjens, I., De Vlaminck, K., Pombo Antunes, A. R., De Prijck, S., Vandamme, N., De Schepper, S., Van Isterdael, G., Scott, C. L., Aerts, J., Berx, G., Boeckxstaens, G. E., Vandenbroucke, R. E., Vereecke, L., Moechars, D., Guilliams, M., Van Ginderachter, J. A., Saeys, Y., & Movahedi, K.
- Affiliations
- Ghent University (BE)
- Vrije Universiteit Brussel (BE)
- Janssen (Belgium) (BE)
- KU Leuven (BE)
- Ghent University Hospital (BE)
- Corresponding author
- Movahedi, Kiavash
- ORCID
- Venue
- Nature Neuroscience
- Published
- 2019-05-06
- Volume
- 22
- Issue
- 6
- Pages
- 1021-1035
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- OpenAlex
- W2943220296
- Cited by
- 1,074
- References
- 68
- Citations by year
- 2026: 160 · 2025: 156 · 2024: 187 · 2023: 152 · 2022: 148 · 2021: 151 · 2020: 90 · 2019: 29
- FWCI
- 46.98
- Type
- journal article
- Language
- en
- Open access
- green
- lirias.kuleuven.be
- Licence
- Locations
- Nature Neuroscience (publishedVersion)
- PubMed (publishedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion)
- Lirias (submittedVersion, other-oa)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Topics
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
- Keywords
- brain macrophages, border-associated macrophages, choroid plexus, dura mater, microglia, IRF8, macrophage ontogeny, postnatal brain development, self-renewal, cerebrospinal fluid
- MeSH terms
- Interferon Regulatory Factor-8, Animals, Brain, Cell Differentiation, Female, Macrophages, Male, Mice, Inbred C57BL, Microglia, Cell Lineage, Interferon Regulatory Factors, Mice
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