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Proteome profiling of the blood brain barrier in mice

ABSTRACT: To characterize the vascular proteome of the brain, proteins were extracted from the brain microvascular fragments isolated from adult mice using CD31-coated magnetic beads. The proteins were enzymatically digested and subjected to mass spectrometric analysis

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Janne Lehtiö

PROVIDER: PXD071189 | JPOST Repository | Fri Aug 07 00:00:00 BST 2026

REPOSITORIES: jPOST

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			Action	DRS
	GACBMM_20170721_TMT_400ugIPG3-10_fr01.raw	Raw
	GACBMM_20170721_TMT_400ugIPG3-10_fr02.raw	Raw
	GACBMM_20170721_TMT_400ugIPG3-10_fr03.raw	Raw
	GACBMM_20170721_TMT_400ugIPG3-10_fr04.raw	Raw
	GACBMM_20170721_TMT_400ugIPG3-10_fr36.raw	Raw

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1 - 5 of 20

Publications

A reference protein atlas of the adult mouse brain vasculature.

He Liqun L Johansson Henrik J HJ Vazquez-Liebanas Elisa E Liu Jianping J Muhl Lars L Nahar Khayrun K Vanlandewijck Michael M Lehtiö Janne J Betsholtz Christer C Andaloussi Mäe Maarja M

Proceedings of the National Academy of Sciences of the United States of America 20260804 32

Current methods for assessing low-abundance proteins in individual cells are limited. As a result, cell functions are often inferred from single-cell RNA sequencing (scRNA-seq) data, which can be misleading due to the poor cross-gene correlation (different genes in the same cells) between messenger RNA (mRNA) and protein levels. To address this issue, we used isolated brain vascular fragments to study the blood-brain barrier. We applied a combination of deep bulk proteomic analysis, a proteomic ...[more]

PMID: 42550898

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A single nuclear transcriptomic characterization of mechanisms responsible for impaired angiogenesis and blood-brain barrier function in Alzheimer’s disease

Project description:Brain perfusion and blood-brain barrier (BBB) integrity are reduced early in Alzheimer’s disease (AD). We performed single nucleus RNA sequencing of vascular cells isolated from AD and non-diseased control brains to characterize pathological transcriptional signatures responsible for this. We found that endothelial cells (EC) are enriched for expression of genes associated with susceptibility to AD. Increased β-amyloid is associated with BBB impairment and a dysfunctional angiogenic response related to a failure of increased pro-angiogenic HIF1A to increased VEGFA signalling to EC. This is associated with vascular inflammatory activation, EC senescence and apoptosis. Our genomic dissection of vascular cell risk gene enrichment provides evidence for a causal role of EC pathology in AD and suggests that reducing vascular inflammatory activation and restoring effective angiogenesis could reduce vascular dysfunction contributing to the genesis or progression of early AD.

2024-01-20 | GSE252921 | GEO

Blood-brain barrier proteomics

Project description:Brain microvessels (BMVs) were isolated from frozen human and mouse cerebral cortices, as well as frozen mouse cerebrums. BMVs and cultured brain microvascular endothelial cells (BMECs), such as hCMEC/D3, HBMEC/ci, and primary BMECs, were analyzed via data-independent acquisition using liquid chromatography-mass spectrometry.

2025-07-23 | PXD060008 | JPOST Repository

Loss of Angiopoietin-2 leads to region-specific brain malformations and blood-brain barrier leakage

Project description:Angiopoietin-2 (ANGPT2) is known to destabilize vascular barriers in most peripheral organs; however, its role in the brain vasculature remains poorly understood. To investigate its physiological function within the brain vasculature, we analyzed constitutive Angpt2 knockout (KO) mice in adulthood. We show that loss of ANGPT2 leads to region-specific vascular malformations and blood-brain barrier (BBB) dysfunction, resulting in differential permeability to 1 kDa and 70 kDa fluorescent tracers. Notably, overt vascular malformations appeared only in select brain regions that allowed leakage of both tracers. These malformations were characterized by dilated, intertwined, and sprouting endothelial cells, surrounded by reactive perivascular cells, along with high levels of astrocyte- and neuron-derived vascular endothelial growth factor A (VEGFA) and elevated expression of the vascular receptors VEGF receptor 2 (KDR) and neuropilin 1 (NRP1). Other cortical areas without obvious malformations exhibited significant leakage of the 1 kDa tracer. We also demonstrate that different cell types take up the tracers after passing the BBB. Our findings identify ANGPT2 as an important factor involved in the regulation of cerebrovascular architecture, barrier integrity, and endothelial–parenchymal interactions, and uncover surprising differences in the leakage patterns and cellular uptake of two widely used BBB tracers.

2026-02-06 | GSE317102 | GEO

BBBomics - Human Blood Brain Barrier Transcriptomics Hub [RNA-seq]

Project description:Functional and structural dysfunction of the blood brain barrier (BBB) leads to severe alterations in brain physiology and is believed to trigger neurodegeneration. To investigate the molecular mechanisms driving the BBB dysfunction, very few human BBB cell culture models are available; of which, the human microvascular endothelial cell line (hCMEC/D3) is the most widely used. Thus far, array-based approaches or targeted seqeuncing based approaches have been employed to characterize the gene expression of the hCMEC/D3 model. However,The goal of this study is to perform deep transcriptomic sequencing of the BBB cell line and obtain features like gene expression, expressed single nucleotide variants, alternate splice forms, circular RNAs, long non-coding RNAs and micro RNAs. We have developed blood brain barriers transcriptomics landscape using RNA sequencing and micro RNA seqeuncing data obtained from replicates of hCMEC/D3 BBB cell line.

2016-03-17 | E-GEOD-76528 | biostudies-arrayexpress

BBBomics - Human Blood Brain Barrier Transcriptomics Hub [miRNA-seq]

Project description:Functional and structural dysfunction of the blood brain barrier (BBB) leads to severe alterations in brain physiology and is believed to trigger neurodegeneration. To investigate the molecular mechanisms driving the BBB dysfunction, very few human BBB cell culture models are available;of which, the human microvascular endothelial cell line (hCMEC/D3) is the most widely used. Thus far, array-based approaches or targeted seqeuncing based approaches have been employed to characterize the gene expression of the hCMEC/D3 model. However,The goal of this study is to perform deep transcriptomic sequencing of the BBB cell line and obtain features like gene expression, expressed single nucleotide variants, alternate splice forms, circular RNAs, long non-coding RNAs and micro RNAs. We have developed blood brain barriers transcriptomics landscape using RNA and micro RNA sequencing data obtained from replicates of hCMEC/D3 BBB cell line.

2016-03-17 | E-GEOD-76530 | biostudies-arrayexpress

The secreted neuronal signal Spock1 regulates the blood-brain barrier

Project description:The blood-brain barrier (BBB) is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick-quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally-expressed Spock1 is cell non-autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix (ECM), increased endothelial transcytosis, and altered pericyte-endothelial interactions. Furthermore, a single dose of recombinant SPOCK1 into spock1 mutants quenches gelatinase activity, restores vascular expression of BBB genes including mcamb, and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM, thereby regulating pericyte-endothelial interactions and downstream vascular gene expression.

2023-05-01 | GSE230236 | GEO

Synergistic induction of blood-brain barrier properties

Project description:Blood–brain barrier (BBB) models derived from human stem cells are powerful tools to improve our understanding of cerebrovascular diseases and to facilitate drug development for the human brain. Yet providing stem cell–derived endothelial cells with the right signaling cues to acquire BBB characteristics while also retaining their vascular identity remains challenging. Here, we show that the simultaneous activation of cyclic AMP and Wnt/β-catenin signaling and inhibition of the TGF-β pathway in endothelial cells robustly induce BBB properties in vitro. To target this interaction, we present a small-molecule cocktail named cARLA, which synergistically enhances barrier tightness in a range of BBB models across species. Mechanistically, we reveal that the three pathways converge on Wnt/β-catenin signaling to mediate the effect of cARLA via the tight junction protein claudin-5. We demonstrate that cARLA shifts the gene expressional profile of human stem cell–derived endothelial cells toward the in vivo brain endothelial signature, with a higher glycocalyx density and efflux pump activity, lower rates of endocytosis, and a characteristic endothelial response to proinflammatory cytokines. Finally, we illustrate how cARLA can improve the predictive value of human BBB models regarding the brain penetration of drugs and targeted nanoparticles. Due to its synergistic effect, high reproducibility, and ease of use, cARLA has the potential to advance drug development for the human brain by improving BBB models across laboratories.

2024-04-18 | GSE224846 | GEO

Brain pericytes and Wnt/β-catenin signaling induce functional blood-brain barrier phenotype in human iPSC-derived model

Project description:The blood-brain barrier (BBB), formed by brain microvascular endothelial cells (BMECs), restricts vascular permeability by establishing tight junctions, reducing vesicular transport, and regulating molecular trafficking via dedicated transporters. In disease, BBB dysfunction leads to barrier disruption and neuroinflammation. Existing human in vitro BBB models recapitulate some but not all of these key BMEC features. Here, we present a method to differentiate human induced pluripotent stem cells (hiPSCs) into BMECs (hiBMECs) by co-culturing hiPSC-derived endothelial cells with brain pericytes (hiBPCs) and activating the Wnt/β-catenin pathway. The resulting hiBMECs exhibit barrier properties, functional efflux transporters, and appropriate inflammatory responses. RNA sequencing revealed a transcriptomic profile in hiBMECs closely matching the adult human BBB. Mechanistically, hiBPCs and Wnt/β-catenin signaling provided complementary cues that converged on ETS1, SMAD3/4, and PPARγ transcriptional networks. These findings reveal a synergistic mechanism by which brain pericytes and Wnt/β-catenin signaling orchestrate human BMEC differentiation and function, providing mechanistic insight into human BBB development and an improved hiPSC-derived BBB model for future drug screening and disease modeling.

2025-08-28 | GSE305015 | GEO

RNA sequencing of adult mouse brain microvascular fragments

Project description:RNA sequencing of adult mouse brain microvascular fragments

| PRJNA1456436 | ENA

BBBomics - Human Blood Brain Barrier Transcriptomics Hub [miRNA-seq]

Project description:Functional and structural dysfunction of the blood brain barrier (BBB) leads to severe alterations in brain physiology and is believed to trigger neurodegeneration. To investigate the molecular mechanisms driving the BBB dysfunction, very few human BBB cell culture models are available;of which, the human microvascular endothelial cell line (hCMEC/D3) is the most widely used. Thus far, array-based approaches or targeted seqeuncing based approaches have been employed to characterize the gene expression of the hCMEC/D3 model. However,The goal of this study is to perform deep transcriptomic sequencing of the BBB cell line and obtain features like gene expression, expressed single nucleotide variants, alternate splice forms, circular RNAs, long non-coding RNAs and micro RNAs.

2016-03-17 | GSE76530 | GEO

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