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A molecular atlas of cell types and zonation in the brain vasculature
Open accessAbstract
Cerebrovascular disease is the third most common cause of death in developed countries, but our understanding of the cells that compose the cerebral vasculature is limited. Here, using vascular single-cell transcriptomics, we provide molecular definitions for the principal types of blood vascular and vessel-associated cells in the adult mouse brain. We uncover the transcriptional basis of the gradual phenotypic change (zonation) along the arteriovenous axis and reveal unexpected cell type differences: a seamless continuum for endothelial cells versus a punctuated continuum for mural cells. We also provide insight into pericyte organotypicity and define a population of perivascular fibroblast-like cells that are present on all vessel types except capillaries. Our work illustrates the power of single-cell transcriptomics to decode the higher organizational principles of a tissue and may provide the initial chapter in a molecular encyclopaedia of the mammalian vasculature.
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In the citing paper
“many of which were well documented61–66.”
From A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain (2023) · cites this paper as [64]
In the citing paper
“We identified endothelial ICs (Figure 2E) with strong contributions from genes with arterial (IC 5 and 20) and veinous (IC 3 and 12) expression, suggesting heterogeneity related to vessel type”
From Molecular diversity and specializations among the cells of the adult mouse brain (2018) · cites this paper as Vanlandewijck et al., 2018
In the citing paper
“These genes (e.g. Tm4sf1 and Slc38a5) showed continuous, reciprocal expression (Data S4G), consistent with the smooth molecular transitions described for endothelial cells associated with arteries or veins”
From Molecular diversity and specializations among the cells of the adult mouse brain (2018) · cites this paper as Vanlandewijck et al., 2018
In the citing paper
“IC 19 represented this difference in a graded rather than categorical way, as Rgs5/Acta2 expression and IC cell scores were continuously, rather than bimodally, distributed across these cells”
From Molecular diversity and specializations among the cells of the adult mouse brain (2018) · cites this paper as Vanlandewijck et al., 2018
In the citing paper
“Among SMA cells, Acta2 expression correlates with a veinous versus arterial distribution”
From Molecular diversity and specializations among the cells of the adult mouse brain (2018) · cites this paper as Vanlandewijck et al., 2018
In the citing paper
“A single IC (IC 13) appeared to encode this distinction, with pericyte marker Vtn as the strongest loading gene”
From Molecular diversity and specializations among the cells of the adult mouse brain (2018) · cites this paper as Vanlandewijck et al., 2018
In the citing paper
“Like Vanlandewijck et al., we observed (Figure 5) distinct endothelial cell types carrying known arterial (e.g., Bmx; VECA) and venous (Slc38a5; VECV) markers, as well as capillary endothelial cells (VECC) expressing Meox1.”
From Molecular Architecture of the Mouse Nervous System (2018) · cites this paper as Vanlandewijck et al., 2018
In the citing paper
“Vanlandewijck et al. described two brain fibroblast-like cell types expressing fibril-forming collagens (e.g., Col1a1, Col1a2), collagen fiber crosslinking proteins (Lum, Dcn), and the platelet-derived growth factor receptor alpha, Pdgfra, which was interposed between astrocyte endfeet and vascular endothelial cells.”
From Molecular Architecture of the Mouse Nervous System (2018) · cites this paper as Vanlandewijck et al., 2018
In the citing paper
“In vivo, αSMA and calponin expression are restricted to mural cells along brain arterioles and arteries [38], however, these markers are often upregulated during culture [39], complicating identification of pericytes.”
From Role of iPSC-derived pericytes on barrier function of iPSC-derived brain microvascular endothelial cells in 2D and 3D (2019) · cites this paper as [38]
In the citing paper
“APOE in the brain is primarily synthesized by astrocytes and microglia, as indicated by a recent single cell RNA-seq study in the mouse (610).”
From Blood-Brain Barrier: From Physiology to Disease and Back (2019) · cites this paper as [610]
In the citing paper
“Pericytes, SMCs, and endothelial cells express thousands of transcripts encoding different transporters, receptors, active efflux pumps, ion channels, and regulatory molecules (28, 72, 86, 129, 242, 358, 359, 610, 675, 678), whose expression pattern varies by zonation along the arteriocapillary-venous axis and cell type (610).”
From Blood-Brain Barrier: From Physiology to Disease and Back (2019) · cites this paper as [610]
In the citing paper
“In contrast to the BBB endothelium's gradual phenotypic change along the arteriovenous axis, mural cells formed two distinct groups comprising pericyte and venous SMCs, and arterial and arteriole SMCs (610).”
From Blood-Brain Barrier: From Physiology to Disease and Back (2019) · cites this paper as [610]
In the citing paper
“Briefly, this study is the first to report that at the BBB endothelium transcription factors predominated at arteries and arterioles, transporters predominated capillaries and veins, and ribosomal proteins indicative of protein synthesis were spread along the arteriovenous axis (610), yielding important insights to biological functions and endothelial specialization along the brain vasculature”
From Blood-Brain Barrier: From Physiology to Disease and Back (2019) · cites this paper as [610]
In the citing paper
“According to a transcriptomic analysis of cells in the vasculature, Plcg2 seems to be expressed in certain subtypes of endothelial cells, although at lower level than compared to microglia (http://betsholtzlab.org/VascularSingleCells/database.html [43]).”
From Alzheimer’s disease phospholipase C-gamma-2 (PLCG2) protective variant is a functional hypermorph (2019) · cites this paper as [43]
In the citing paper
“we used an siRNA sequence targeting Ppib because this gene is abundantly and ubiquitously expressed across CNS cell types [27].”
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 [27]
In the citing paper
“Here, we used an siRNA sequence targeting Ppib because this gene is abundantly and ubiquitously expressed across CNS cell types.34”
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 [34]
In the citing paper
“WAVE2 is expressed at high levels in microglia and vascular endothelial cells14,15.”
From The WAVE complex in developmental and adulthood brain disorders (2025) · cites this paper as [14]
In the citing paper
“In addition to astrocytes and microglia, other cell types in the brain have been reported to produce ApoE under different conditions. These cells include oligodendrocytes, pericytes, vascular smooth muscle cells, perivascular fibroblasts, and perivascular macrophages [107–109].”
From ApoE lipoproteins in the central nervous system under homeostasis and role in Alzheimer’s disease and related disorders (2026) · cites this paper as [108]
In the citing paper
“PDGFRβ expression in pericytes is noticeably higher than in SMCs18,25,26.”
From Blood–brain barrier breakdown is an early biomarker of human cognitive dysfunction (2019) · cites this paper as [25]
In the citing paper
“Based on marker gene enrichment (Table S1), Endo.1 may correspond to endothelial capillary cells, Endo.2 to venous endothelial cells, and Endo.3 to arterial endothelial cells (Vanlandewijck et al., 2018).”
From Single-Cell Analysis of Regional Differences in Adult V-SVZ Neural Stem Cell Lineages (2019) · cites this paper as Vanlandewijck et al., 2018
In the citing paper
“We spatially mapped the developing arterio-venous zonation in the embryonic LV ChP in whole explants by combining the pan-endothelial marker PECAM1 with markers for arteries (Acta2+, Vwf+) and veins (Acta2−, Vwf+) (Vanlandewijck et al., 2018).”
From A cellular and spatial map of the choroid plexus across brain ventricles and ages (2021) · cites this paper as Vanlandewijck et al., 2018
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Self-citationA perivascular perspective on the immune impacts in cerebral amyloid angiopathy
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“These markers suggested a more contractile phenotype consistent with mural cell function [20, 21] and are consistent with localization along pre-and post-capillary segments where transitional features between pericytes and smooth muscle-like mural cells can occur.”
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“The cellular and molecular profile of brain vasculature has been investigated in both species (Vanlandewijck et al., 2018; Wälchli et al., 2024; Yang et al., 2022).”
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“Message for both of these channels has been detected in brain pericytes, with Trpc3 transcripts being particularly abundant (18–20).”
InfluentialNeutrophil‐Mimetic MRI Enables Ultra‐Early Detection of Vascular Inflammation After Stroke
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Cohen, C. E., Párraga-Leo, A., Rodríguez-Montes, L., Kim, C. E., Moullet, M., Paredes, A., Lorenzi, V., Vilarrasa‐Blasi, R., Predeus, A. V., Polański, K., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.10.731198
MCC links Wnt/PCP signaling to endothelial polarity and vascular remodeling
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“Analysis of the Betsholtz vascular atlas [48, 49] showed Mcc expression enriched in brain and lung ECs, with minimal expression in mural or perivascular cells (Supplementary Fig.”
Londoño, C. J., & Zheng, B. (2026) · Cells · doi:10.3390/cells15131135 · Cited by 1
“In the context of SCI, perivascular cells isolated from PDGFR β + /NG2 + mice validated vitronectin (Vtn) as a pericyte-specific gene [36], a finding supported by subsequent scRNA-seq datasets [17,18,35,37].”
InfluentialSkin capillary endothelial cells form a network of spatiotemporally conserved Ca 2+ activity
Swaminathan, A., Gonzalez, D. G., Matte-Martone, C. C., Xu, F., Simpson, D., Moore, J. L., Lin, Z., Rana, U., Alonso, D. M., Mack, J. J., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2519708123
“L - type VGCCs are known to be expressed in mural cells, including pericytes (58–61), but not endothelial cells (51, 52).”
Meneses, L. K., Kim, H., Szot, G. L., Sneddon, J. B., & Gartner, Z. J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.30.733275
“Published human vascular transcriptomic datasets and experimental vascular models have demonstrated that pericytes express BM-associated genes and participate in vascular matrix deposition[20, 21].”
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Vascular reprogramming in cancer: engineering the tumor microenvironment
Nishimura, Y. (2026) · Human Cell · doi:10.1007/s13577-026-01417-w
“Within this ecosystem, tumor endothelial cells exist in multiple interconvertible states, including angiogenic tip-and stalk-like phenotypes, quiescent endothelial populations, metabolically specialized subsets, and immunoregulatory endothelial programs [45].”
Noterman, M. F., Sancho, M., de la Cruz, S. H., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2615120123
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“31 A recent single-cell transcriptome study in mice 32 demonstrated that both Esr1 and Esr2 are expressed in brain ECs, however, Esr1 is more abundantly and widely expressed in different EC types in mouse brain than Esr2 (Supplemental Figure I).”
Diverse roles of connexins in the neuro-vasculature in homeostasis and disease
Delobel, V., Genet, N., & Hirschi, K. K. (2026) · Translational Neuroscience · doi:10.1515/tnsci-2025-0400
Leaky Blood–Brain Barrier and Chronic Pain: The Neuroinflammatory Link
García-Domínguez, M. (2026) · Biology · doi:10.3390/biology15141145
“…during neurovascular development via reciprocal signaling between neural progenitors and endothelial precursors, leading to a stable transcriptional and epigenetic program characterized by sustained expression of barrier-associated genes and suppression of permeable endothelial signatures [47,48].”
Bjørnholm, K. D., Li, H., Gaudio, F. D., Mocci, G., Shao, W., Baldisseri, E., Rao, S. B., Lindblad, C., Fletcher‐Sandersjöö, A., Vázquez-Liébanas, E., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-75367-0
Self-citationProgranulin haploinsufficiency remodels the cerebral microvasculature and neurovascular unitPreprint
Chakraborty, S., Weick, M., Franciosa, S. A., Tabrizi, Z., Swinehart, C., Moore, G. R., Lee, D., Bhatt, N. N., Cano, A., Poorva, P., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.20.738719
“Endothelial nuclei were assigned to arterial, capillary and venous segments using canonical zonation markers 78,94,95 , and differential expression between FTD-GRN and control capillary endothelial nuclei (1,981 FTD-GRN and 2,104 control nuclei) was tested with MAST (Seurat, FindMarkers),…”
Bandke, D., & Langer, R. (2026) · Cancers · doi:10.3390/cancers18152397
“Pial cells and perivascular fibroblasts (PVFs) are transcriptionally very similar, if not identical [42].”
What Is the Role of Endothelial Cells in Cerebral Blood Flow Dysregulation in Small Vessel Disease?
Benarroch, E. E. (2026) · Neurology · doi:10.1212/wnl.0000000000218477
Endothelial cell–pericyte interactions in ischemic stroke: From microvascular pathology to repair
Feng, S., Zhang, C., Zhao, Y., Wang, Y., 张柏民, Zhang, Q., Zheng, Y., Cheng, F., Li, C., Wang, X., et al. (2026) · Pharmacological Research · doi:10.1016/j.phrs.2026.108351
Endothelial Cell-Pericyte Crosstalk in the Brain Balances Microvascular Stability and Plasticity
Lee, J. M., Luc, E., & Stratman, A. N. (2026) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.126.323547
Wang, Y., Su, C., Chen, T., Chen, S., Li, Z., & Zhang, L. (2026) · Journal of Integrative Neuroscience · doi:10.31083/jin51032
A reference protein atlas of the adult mouse brain vasculature
He, L., Johansson, H. J., Vázquez-Liébanas, E., Liu, J., Muhl, L., Nahar, K., Vanlandewijck, M., Lehtiö, J., Betsholtz, C., & Mäe, M. A. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2614173123 · Cited by 1
“In the context of blood vessels in the brain, scRNA - seq has provided insights into the molecular nature of the blood–brain barrier (BBB), AV zonation of both ECs and surrounding mural cells, and helped define vessel - associated fibroblasts (3, 4).”
Self-citationIdentifying Pulmonary Endothelial Cell Zonation From Single-Cell Transcriptomics
Sveiven, S., Knutsen, C., Zanini, F., Cornfield, D. N., & Alvira, C. M. (2026) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.126.324377
Phagocytic activity of perivascular cell promotes CNS injury pathologyPreprint
Zhou, T., Zhang, Z., Zeng, F., Song, H., Xu, Z., Hu, Z., Yao, L., Wang, W., Zhang, T., Du, X., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.03.742479
Self-citationKazanis, I., Silva, M. E., de la Fuente, A. G., de Castro, F., & Rivera, F. J. (2026) · Acta Physiologica · doi:10.1111/apha.70285
“While vSMCs and PVFs localize in arteries, arterioles, venules and veins, PCs are restricted to microvessels (capillaries) [18–20].”
Guo, Q., Yao, Y., Ding, Y., Chen, L., Zhang, Q., Zhang, H., & Xue, J. (2026) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2026.1899684 · Cited by 1
“Importantly, this crosstalk is highly context-dependent, often associated with distinct vascular phenotypes under metabolic, neurovascular, and tumor-associated conditions (Armulik et al., 2011; Sweeney et al., 2016; Vanlandewijck et al., 2018b; Zlokovic, 2011).”
Cerebral Intramural Cells: A Missing Cellular Link Between Vascular Aging and Alzheimer’s Disease
Arbănași, E. M., Arbănași, E. M., Boghițoiu, T., Cărare, S. A., Cordoș, B. A., Braysh, K., Suciu, N., Chinezu, L., Manu, D. R., Montagne, A., et al. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27167353
“…phenotype along the arterio–capillary– venous axis, moving from pial SMCs to ensheathing pericytes and capillary pericytes to venular mural cells, a pattern supported by single-cell transcriptomic zonation studies but obscured when the NVU is treated as a single functional unit [36,45].”
InfluentialThe role of nervous system extracellular matrix remodeling in chronic pain
Alhamwi, A., Anits, E., & Krock, E. (2026) · Pain · doi:10.1097/j.pain.0000000000004089
Defining a leptomeningeal blood–cerebrospinal fluid barrier as a specialized vascular interfacePreprint
Seegren, P. V. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.19.745529
The role of microglia glucose metabolism reprogramming in Alzheimer's disease treatment
Cao, Q., Shen, M., Liu, Y., Li, C., Liu, L., Zhou, J., Yue, R., Niu, D., Ren, Y., Pan, L., et al. (2026) · Journal of Alzheimer s Disease · doi:10.1177/13872877261478594
Brain pericytes exhibit spatially organized and dynamically regulated molecular heterogeneityPreprint
Huang, S., Glandorf, L., Sauvageot, S., Glück, C., Preuss, H., Droux, J., Maheshwari, U., Sridhar, S., Wegener, S., Weber, B., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.17.745290
“We obtained gene expression profiles of mouse brain vascular cells from three scRNA-seq datasets: Vanlandewijck et al. 17 , Yao et al. 31 , and Smith et al. 19 (S.Table 1).”
InfluentialSelf-citationA tissue-resolved endothelial surface proteome atlas informs organ-selective vascular targetingPreprint
Deng, Y., Li, H., Meng, J., Lemoff, A. S., Zhou, H., Pi, X., & Zhu, Y. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.21.746320
“These studies have revealed arterial, venous, and capillary programs, as well as highly specialized endothelial populations such as the blood-brain barrier (BBB) and glomerular endothelium [11, 12].”
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“JAM2, along with other proteins from the tight-junction protein family (such as JAM3, Occludin, and Claudin-5), is highly expressed in the brain [16], and is believed to play a crucial role in maintaining the stability of the blood – brain barrier (BBB) [17 – 19].”
Loss of laminin-γ1 in pericytes impairs microvascular function and cognition
Ruan, J., Nasrollahi, A., Martin, C., Asgari, M., Shih, A. Y., & Yao, Y. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117904 · Cited by 2
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Self-citationCell-to-Cell Signaling Networks at the Blood-Brain Barrier in Health and Disease
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VINE-seq and MultiVINE-seq for single-nucleus and multiome profiling of the brain vasculature
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Niche cell positioning drives functional heterogeneity in the Drosophila testis stem cell niche
Viveiros, J. M., & Matunis, E. L. (2026) · Genetics · doi:10.1093/genetics/iyag244
Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution
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AKAP12 Regulates Perivascular OPC Accumulation in the Corpus Callosum During Cerebral Hypoperfusion
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“This spatial organization may also be consistent with prior vascular atlas studies (Vanlandewijck et al. 2018), as our re-analysis of the dataset confirmed the presence of OPCs positioned adjacent to vascular structures (data not shown).”
Wu, C., Ye, X., Chen, H., Fang, Y., Lan, Y., Ye, J., Liu, X., Xiao, R., Zhu, S., & Huang, S. (2026) · Alzheimer s & Dementia · doi:10.1002/alz.71858
Brain Aging and Cellular Senescence Trigger Neuroimmunological Dysregulation and Neurodegeneration
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Metadata
- Authors
- Vanlandewijck, M., He, L., Mäe, M. A., Andrae, J., Ando, K., Del Gaudio, F., Nahar, K., Lebouvier, T., Laviña, B., Gouveia, L., Sun, Y., Raschperger, E., Räsänen, M., Zarb, Y., Mochizuki, N., Keller, A., Lendahl, U., & Betsholtz, C.
- Affiliations
- Uppsala University (SE)
- Tianjin Medical University General Hospital (CN)
- Karolinska Institutet (SE)
- University of Zurich (CH)
- Japan Agency for Medical Research and Development (JP)
- Corresponding author
- Betsholtz, Christer
- ORCID
- Venue
- Nature
- Published
- 2018-02-14
- Volume
- 554
- Issue
- 7693
- Pages
- 475-480
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2786318872
- Semantic Scholar
- 237e37a314d2faef1d389b147614e8fa550a3087
- Cited by
- 1,892
- References
- 65
- Citations by year
- 2026: 197 · 2025: 244 · 2024: 275 · 2023: 234 · 2022: 258 · 2021: 271 · 2020: 222 · 2019: 125 · 2018: 65
- FWCI
- 74.80
- Type
- journal article
- Language
- en
- Update notices
- correction (2018-06-20)
- Open access
- green
- hdl.handle.net
- Licence
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Työväentutkimus Vuosikirja (submittedVersion, other-oa)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (159514)
- Topics
- Life Sciences › Neuroscience › Neurology › Barrier Structure and Function Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Health Sciences › Medicine › Clinical Neurology › Cerebrovascular and genetic disorders
- Keywords
- cerebral vasculature, blood-brain barrier, endothelial cells, mural cells, pericytes, smooth muscle cells, perivascular cells, single-cell transcriptomics, cerebrovascular disease, mouse brain
- MeSH terms
- Animals, Arteries, Arterioles, Blood Vessels, Brain, Capillaries, Female, Fibroblasts, Male, Organ Specificity, Veins, Pericytes, Myocytes, Smooth Muscle, Endothelial Cells, Mice, Single-Cell Analysis, Transcriptome
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