Michael Vanlandewijck

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 ruler approach, and scRNA-seq, assuming a high within-gene correlation (same gene in different cells) between mRNA and protein. This approach allowed us to estimate protein copy numbers per cell for 9,940 proteins across eight cell types, including endothelium, smooth muscle, pericytes, fibroblasts, and microglia. We also evaluated protein abundance in astrocyte end-feet attached to the vessel fragments. Our data are available through an Online Database, providing a searchable resource and reference protein atlas for future studies of neurovascular proteomics in health and disease.

The extent to which the cerebrovasculature is affected in various brain disorders is still not well understood. To address this, we established a transcriptomic repository of major vascular cell types and microglia to compare the global transcriptomic response in mouse models of three human brain disorders linked to neuroinflammation and associated vascular reactivity: Alzheimer’s disease (AD), traumatic brain injury (TBI), and cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). Single-cell analysis of >250,000 cells at different disease stages led to identification of two previously unknown vascular cell subtypes, expanded the endothelial zonation spectrum and allowed for a detailed analysis of the cellular and molecular responses. Surprisingly, most vascular cell types lacked major transcriptomic changes across the three conditions, while microglia exhibited significant, disease-specific transcriptional changes. Notably, microglial responses converged between late-stage TBI and AD, offering insights into the predisposition for neurodegeneration following TBI.

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 mice in adulthood. We showed 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 demonstrated that different cell types took up the tracers after passing the BBB. Our findings identified ANGPT2 as an important factor involved in the regulation of cerebrovascular architecture, barrier integrity, and endothelial-parenchymal interactions, and uncovered surprising differences in the leakage patterns and cellular uptake of two widely used BBB tracers.

The liver plays crucial roles in many essential physiological processes, and its impaired function due to liver fibrosis from various causes is an increasingly significant health issue. The liver’s functionality relies on the precise arrangement of its cellular structures, yet the molecular architecture of these units remains only partially understood. We created a comprehensive molecular atlas detailing the major cell types present in the adult mouse liver through deep single-cell RNA sequencing. Our analysis offers new insights into hepatic endothelial and mesenchymal cells, specifically highlighting the diversity of cells in the periportal microvasculature, the sinusoids, and the portal vein, the latter exhibiting a mixed arterio-venous phenotype. We identified distinct subpopulations of hepatic stellate cells, fibroblasts, and vascular mural cells located in different anatomical liver regions. Comparisons with transcriptomic data from disease models indicate that a previously unrecognized capsular population of hepatic stellate cells expands in response to fibrotic disease. Our findings reveal that various fibroblast subpopulations respond differently to pathological insults. This data resource will be relevant for the advancement of therapies targeting hepatic diseases.

The liver plays a crucial role in essential physiological processes, and its impaired function due to liver fibrosis from various causes is an increasingly significant health issue. The liver’s functionality relies on the precise arrangement of its cellular structures, yet the molecular architecture of these units remains only partially understood. We created a comprehensive molecular atlas detailing all the major cell types present in the adult mouse liver through deep single-cell RNA sequencing. Our analysis offers new insights into hepatic endothelial and mesenchymal cells, specifically highlighting the differences between the cells of the periportal microvasculature, the sinusoids, and the portal vein, the latter exhibiting a mixed arterio-venous phenotype. We identified distinct subpopulations of hepatic stellate cells, fibroblasts, and vascular mural cells located in different anatomical regions. Comparisons with transcriptomic data from disease models indicate that a previously unrecognized capsular population of hepatic stellate cells expands in response to fibrotic disease. Our findings reveal that various fibroblast subpopulations respond differently to pathological insults. This data resource will be invaluable for advancing therapeutic interventions targeting hepatic diseases.

BACKGROUND: While our understanding of the single-cell gene expression patterns underlying the transformation of vascular cell types during the progression of atherosclerosis is rapidly improving, the clinical and pathophysiological relevance of these changes remains poorly understood. METHODS: Single-cell RNA sequencing data generated with SmartSeq2 (≈8000 genes/cell) in 16 588 single cells isolated during atherosclerosis progression in Ldlr ^−/− Apob ^100/100 mice with human-like plasma lipoproteins and from humans with asymptomatic and symptomatic carotid plaques was clustered into multiple subtypes. For clinical and pathophysiological context, the advanced-stage and symptomatic subtype clusters were integrated with 135 tissue-specific (atherosclerotic aortic wall, mammary artery, liver, skeletal muscle, and visceral and subcutaneous, fat) gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients in the STARNET (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task) study. RESULTS: Advanced stages of atherosclerosis progression and symptomatic carotid plaques were largely characterized by 3 smooth muscle cells (SMCs), and 3 macrophage subtype clusters with extracellular matrix organization/osteogenic (SMC), and M1-type proinflammatory/Trem2-high lipid-associated (macrophage) phenotypes. Integrative analysis of these 6 clusters with STARNET revealed significant enrichments of 3 arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage) with major contributions to coronary artery disease heritability and strong associations with clinical scores of coronary atherosclerosis severity. The presence and pathophysiological relevance of GRN39 were verified in 5 independent RNAseq data sets obtained from the human coronary and aortic artery, and primary SMCs and by targeting its top-key drivers, FRZB and ALCAM in cultured human coronary artery SMCs. CONCLUSIONS: By identifying and integrating the most gene-rich single-cell subclusters of atherosclerosis to date with a coronary artery disease framework of GRNs, GRN39 was identified and independently validated as being critical for the transformation of contractile SMCs into an osteogenic phenotype promoting advanced, symptomatic atherosclerosis.

Oncogenic mutations in PIK3CA, encoding p110α-PI3K, are a common cause of venous and lymphatic malformations. Vessel type–specific disease pathogenesis is poorly understood, hampering development of efficient therapies. Here, we reveal a new immune-interacting subtype of Ptx3-positive dermal lymphatic capillary endothelial cells (iLECs) that recruit pro-lymphangiogenic macrophages to promote progressive lymphatic overgrowth. Mouse model of Pik3caH1047R-driven vascular malformations showed that proliferation was induced in both venous and lymphatic ECs but sustained selectively in LECs of advanced lesions. Single-cell transcriptomics identified the iLEC population, residing at lymphatic capillary terminals of normal vasculature, that was expanded in Pik3caH1047R mice. Expression of pro-inflammatory genes, including monocyte/macrophage chemokine Ccl2, in Pik3caH1047R-iLECs was associated with recruitment of VEGF-C–producing macrophages. Macrophage depletion, CCL2 blockade, or anti-inflammatory COX-2 inhibition limited Pik3caH1047R-driven lymphangiogenesis. Thus, targeting the paracrine crosstalk involving iLECs and macrophages provides a new therapeutic opportunity for lymphatic malformations. Identification of iLECs further indicates that peripheral lymphatic vessels not only respond to but also actively orchestrate inflammatory processes.

Vascular malformations are congenital, chronically debilitating diseases. Somatic oncogenic mutations in PIK3CA , encoding p110α-PI3K, specifically cause venous and lymphatic malformations (LM), yet the basis of vessel type-restricted disease manifestation is unknown. Here we report endothelial subtype-specific responses to the common causative Pik3ca ^H1047R mutation, and reveal a new immunoregulatory subtype of dermal lymphatic capillary endothelial cells (iLECs) as a driver of LM pathology. Mouse model of Pik3ca ^H1047R -driven vascular malformations showed that cell proliferation was a common early response of venous and lymphatic ECs to oncogenic Pik3ca , but sustained selectively in LECs of advanced lesions. Lymphatic overgrowth was associated with increased pro-inflammatory cytokine levels and pro-lymphangiogenic myeloid cell infiltrate. Single-cell transcriptomics revealed a new LEC subtype at capillary terminals, characterized by the expression of immunoregulatory genes. Selective expansion and activation of iLECs in the Pik3ca ^H1047R mice was evidenced by proliferation and upregulation of pro-inflammatory genes. Importantly, macrophage depletion or anti-inflammatory COX-2 inhibition limited Pik3ca ^H1047R -driven lymphangiogenesis. This provides a therapeutic target for LM and suggests a paracrine crosstalk in which LEC-autonomous oncogenic Pik3ca signaling induces immune activation that in turn sustains pathological lymphangiogenesis. Identification of iLECs indicates that peripheral lymphatic vessels not only respond to inflammation but also actively orchestrate the immune response.

The blood-brain barrier (BBB) is central to separate blood from the extracellular fluids of the brain. To understand disease-related changes in the BBB is pivotal and such changes can increasingly be studied by single-cell RNA sequencing (scRNAseq), which provides high-resolution insight into gene expression changes related to the pathophysiological response of the vasculature. However, analysis of the vascular cells in the brain is challenging due to the low abundance of these cells relative to neuronal and glial cells, and improved techniques for enrichment of the vascular component is therefore warranted. The present study describes a method whereby panning with CD31-coated magnetic beads allows isolation of brain vasculature without the need for transgenic reporter lines or FACS sorting. The protocol was tested in three modalities: isolation of cells for scRNAseq, western blot (WB) analysis, and primary cell culture. For scRNAseq, a total of 22,515 single-cell transcriptomes were generated from 12-months old mice and separated into 23 clusters corresponding to all known vascular and perivascular cell types. The most abundant cell type was endothelial cells (EC) ( Pecam1 - and Cdh5 -positive), which dispersed into clusters of arterial, capillary, and venous EC according to previously established BBB arterio-venous zonation markers. Furthermore, we identified clusters of microglia ( Aif1- positive), one cluster of fenestrated endothelial cells ( Plvap -positive; Cldn5 -negative), a cluster of pericytes ( Kcnj8 - and Abcc9- positive) and a cluster of vascular smooth muscle cells (VSMC) ( Acta2 - and Tagln -positive). WB analysis using established markers for the different cell types (CD31 (EC), SM22 (VSMC), PDGFRB (pericytes), GFAP (astrocytes), and IBA1 (microglia) confirmed their presence in the isolated vascular component and suggests that the protocol is suitable for future proteomic analysis. Finally, we adapted the isolation protocol to accommodate primary culture of brain vascular cells. In conclusion, we have successfully established a simple and fast method for isolating microvasculature from the murine brain independent of cell sorting and alleviating the need to use reporter mouse lines. The protocol is suitable for a multitude of testing modalities, including single-cell analyses, WB and primary cell culture.