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1.
Cell ; 180(4): 764-779.e20, 2020 02 20.
Article in English | MEDLINE | ID: mdl-32059779

ABSTRACT

The heterogeneity of endothelial cells (ECs) across tissues remains incompletely inventoried. We constructed an atlas of >32,000 single-EC transcriptomes from 11 mouse tissues and identified 78 EC subclusters, including Aqp7+ intestinal capillaries and angiogenic ECs in healthy tissues. ECs from brain/testis, liver/spleen, small intestine/colon, and skeletal muscle/heart pairwise expressed partially overlapping marker genes. Arterial, venous, and lymphatic ECs shared more markers in more tissues than did heterogeneous capillary ECs. ECs from different vascular beds (arteries, capillaries, veins, lymphatics) exhibited transcriptome similarity across tissues, but the tissue (rather than the vessel) type contributed to the EC heterogeneity. Metabolic transcriptome analysis revealed a similar tissue-grouping phenomenon of ECs and heterogeneous metabolic gene signatures in ECs between tissues and between vascular beds within a single tissue in a tissue-type-dependent pattern. The EC atlas taxonomy enabled identification of EC subclusters in public scRNA-seq datasets and provides a powerful discovery tool and resource value.


Subject(s)
Endothelial Cells/metabolism , Single-Cell Analysis , Transcriptome , Animals , Brain/cytology , Cardiovascular System/cytology , Endothelial Cells/classification , Endothelial Cells/cytology , Gastrointestinal Tract/cytology , Male , Mice , Mice, Inbred C57BL , Muscles/cytology , Organ Specificity , RNA-Seq , Testis/cytology
2.
Cell ; 154(3): 651-63, 2013 Aug 01.
Article in English | MEDLINE | ID: mdl-23911327

ABSTRACT

Vessel sprouting by migrating tip and proliferating stalk endothelial cells (ECs) is controlled by genetic signals (such as Notch), but it is unknown whether metabolism also regulates this process. Here, we show that ECs relied on glycolysis rather than on oxidative phosphorylation for ATP production and that loss of the glycolytic activator PFKFB3 in ECs impaired vessel formation. Mechanistically, PFKFB3 not only regulated EC proliferation but also controlled the formation of filopodia/lamellipodia and directional migration, in part by compartmentalizing with F-actin in motile protrusions. Mosaic in vitro and in vivo sprouting assays further revealed that PFKFB3 overexpression overruled the pro-stalk activity of Notch, whereas PFKFB3 deficiency impaired tip cell formation upon Notch blockade, implying that glycolysis regulates vessel branching.


Subject(s)
Endothelial Cells/metabolism , Glycolysis , Neovascularization, Physiologic , Phosphofructokinase-2/metabolism , Animals , Cell Line, Tumor , Cells, Cultured , Endothelial Cells/cytology , Female , Gene Deletion , Gene Silencing , Humans , Male , Mice , Mice, Inbred C57BL , Phosphofructokinase-2/genetics , Pseudopodia/metabolism , Zebrafish
3.
Nature ; 605(7911): 747-753, 2022 05.
Article in English | MEDLINE | ID: mdl-35585241

ABSTRACT

Cancer metastasis requires the transient activation of cellular programs enabling dissemination and seeding in distant organs1. Genetic, transcriptional and translational heterogeneity contributes to this dynamic process2,3. Metabolic heterogeneity has also been observed4, yet its role in cancer progression is less explored. Here we find that the loss of phosphoglycerate dehydrogenase (PHGDH) potentiates metastatic dissemination. Specifically, we find that heterogeneous or low PHGDH expression in primary tumours of patients with breast cancer is associated with decreased metastasis-free survival time. In mice, circulating tumour cells and early metastatic lesions are enriched with Phgdhlow cancer cells, and silencing Phgdh in primary tumours increases metastasis formation. Mechanistically, Phgdh interacts with the glycolytic enzyme phosphofructokinase, and the loss of this interaction activates the hexosamine-sialic acid pathway, which provides precursors for protein glycosylation. As a consequence, aberrant protein glycosylation occurs, including increased sialylation of integrin αvß3, which potentiates cell migration and invasion. Inhibition of sialylation counteracts the metastatic ability of Phgdhlow cancer cells. In conclusion, although the catalytic activity of PHGDH supports cancer cell proliferation, low PHGDH protein expression non-catalytically potentiates cancer dissemination and metastasis formation. Thus, the presence of PHDGH heterogeneity in primary tumours could be considered a sign of tumour aggressiveness.


Subject(s)
Breast Neoplasms , Neoplasm Metastasis , Phosphoglycerate Dehydrogenase , Animals , Breast Neoplasms/pathology , Cell Line, Tumor , Cell Movement , Cell Proliferation , Disease Progression , Female , Gene Silencing , Humans , Mice , Phosphoglycerate Dehydrogenase/genetics , Serine/metabolism
4.
Nature ; 587(7835): 626-631, 2020 11.
Article in English | MEDLINE | ID: mdl-33116312

ABSTRACT

Muscle regeneration is sustained by infiltrating macrophages and the consequent activation of satellite cells1-4. Macrophages and satellite cells communicate in different ways1-5, but their metabolic interplay has not been investigated. Here we show, in a mouse model, that muscle injuries and ageing are characterized by intra-tissue restrictions of glutamine. Low levels of glutamine endow macrophages with the metabolic ability to secrete glutamine via enhanced glutamine synthetase (GS) activity, at the expense of glutamine oxidation mediated by glutamate dehydrogenase 1 (GLUD1). Glud1-knockout macrophages display constitutively high GS activity, which prevents glutamine shortages. The uptake of macrophage-derived glutamine by satellite cells through the glutamine transporter SLC1A5 activates mTOR and promotes the proliferation and differentiation of satellite cells. Consequently, macrophage-specific deletion or pharmacological inhibition of GLUD1 improves muscle regeneration and functional recovery in response to acute injury, ischaemia or ageing. Conversely, SLC1A5 blockade in satellite cells or GS inactivation in macrophages negatively affects satellite cell functions and muscle regeneration. These results highlight the metabolic crosstalk between satellite cells and macrophages, in which macrophage-derived glutamine sustains the functions of satellite cells. Thus, the targeting of GLUD1 may offer therapeutic opportunities for the regeneration of injured or aged muscles.


Subject(s)
Glutamine/metabolism , Macrophages/metabolism , Muscle, Skeletal/metabolism , Regeneration , Satellite Cells, Skeletal Muscle/metabolism , Aging/metabolism , Amino Acid Transport System ASC/antagonists & inhibitors , Amino Acid Transport System ASC/metabolism , Animals , Cell Differentiation , Cell Proliferation , Female , Glutamate Dehydrogenase/deficiency , Glutamate Dehydrogenase/genetics , Glutamate Dehydrogenase/metabolism , Glutamate-Ammonia Ligase/antagonists & inhibitors , Glutamate-Ammonia Ligase/metabolism , Macrophages/enzymology , Male , Mice , Minor Histocompatibility Antigens/metabolism , Muscle, Skeletal/cytology , Muscle, Skeletal/injuries , Muscle, Skeletal/pathology , Oxidation-Reduction , Satellite Cells, Skeletal Muscle/cytology , TOR Serine-Threonine Kinases
5.
Nature ; 579(7797): 111-117, 2020 03.
Article in English | MEDLINE | ID: mdl-32103177

ABSTRACT

The avascular nature of cartilage makes it a unique tissue1-4, but whether and how the absence of nutrient supply regulates chondrogenesis remain unknown. Here we show that obstruction of vascular invasion during bone healing favours chondrogenic over osteogenic differentiation of skeletal progenitor cells. Unexpectedly, this process is driven by a decreased availability of extracellular lipids. When lipids are scarce, skeletal progenitors activate forkhead box O (FOXO) transcription factors, which bind to the Sox9 promoter and increase its expression. Besides initiating chondrogenesis, SOX9 acts as a regulator of cellular metabolism by suppressing oxidation of fatty acids, and thus adapts the cells to an avascular life. Our results define lipid scarcity as an important determinant of chondrogenic commitment, reveal a role for FOXO transcription factors during lipid starvation, and identify SOX9 as a critical metabolic mediator. These data highlight the importance of the nutritional microenvironment in the specification of skeletal cell fate.


Subject(s)
Bone and Bones/cytology , Cellular Microenvironment , Chondrogenesis , Lipid Metabolism , SOX9 Transcription Factor/metabolism , Stem Cells/cytology , Stem Cells/metabolism , Animals , Bone and Bones/blood supply , Chondrocytes/cytology , Chondrocytes/metabolism , Fatty Acids/metabolism , Female , Food Deprivation , Forkhead Transcription Factors/metabolism , Male , Mice , Mice, Inbred C57BL , Osteogenesis , Oxidation-Reduction , SOX9 Transcription Factor/genetics , Signal Transduction , Wound Healing
6.
Physiol Rev ; 98(1): 3-58, 2018 01 01.
Article in English | MEDLINE | ID: mdl-29167330

ABSTRACT

Endothelial cells (ECs) are more than inert blood vessel lining material. Instead, they are active players in the formation of new blood vessels (angiogenesis) both in health and (life-threatening) diseases. Recently, a new concept arose by which EC metabolism drives angiogenesis in parallel to well-established angiogenic growth factors (e.g., vascular endothelial growth factor). 6-Phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3-driven glycolysis generates energy to sustain competitive behavior of the ECs at the tip of a growing vessel sprout, whereas carnitine palmitoyltransferase 1a-controlled fatty acid oxidation regulates nucleotide synthesis and proliferation of ECs in the stalk of the sprout. To maintain vascular homeostasis, ECs rely on an intricate metabolic wiring characterized by intracellular compartmentalization, use metabolites for epigenetic regulation of EC subtype differentiation, crosstalk through metabolite release with other cell types, and exhibit EC subtype-specific metabolic traits. Importantly, maladaptation of EC metabolism contributes to vascular disorders, through EC dysfunction or excess angiogenesis, and presents new opportunities for anti-angiogenic strategies. Here we provide a comprehensive overview of established as well as newly uncovered aspects of EC metabolism.


Subject(s)
Endothelial Cells/metabolism , Neovascularization, Pathologic/metabolism , Neovascularization, Physiologic/physiology , Vascular Diseases/metabolism , Animals , Epigenesis, Genetic/physiology , Homeostasis/physiology , Humans
7.
Nature ; 565(7740): 511-515, 2019 01.
Article in English | MEDLINE | ID: mdl-30651640

ABSTRACT

Endochondral ossification, an important process in vertebrate bone formation, is highly dependent on correct functioning of growth plate chondrocytes1. Proliferation of these cells determines longitudinal bone growth and the matrix deposited provides a scaffold for future bone formation. However, these two energy-dependent anabolic processes occur in an avascular environment1,2. In addition, the centre of the expanding growth plate becomes hypoxic, and local activation of the hypoxia-inducible transcription factor HIF-1α is necessary for chondrocyte survival by unidentified cell-intrinsic mechanisms3-6. It is unknown whether there is a requirement for restriction of HIF-1α signalling in the other regions of the growth plate and whether chondrocyte metabolism controls cell function. Here we show that prolonged HIF-1α signalling in chondrocytes leads to skeletal dysplasia by interfering with cellular bioenergetics and biosynthesis. Decreased glucose oxidation results in an energy deficit, which limits proliferation, activates the unfolded protein response and reduces collagen synthesis. However, enhanced glutamine flux increases α-ketoglutarate levels, which in turn increases proline and lysine hydroxylation on collagen. This metabolically regulated collagen modification renders the cartilaginous matrix more resistant to protease-mediated degradation and thereby increases bone mass. Thus, inappropriate HIF-1α signalling results in skeletal dysplasia caused by collagen overmodification, an effect that may also contribute to other diseases involving the extracellular matrix such as cancer and fibrosis.


Subject(s)
Bone Diseases/metabolism , Bone Diseases/pathology , Chondrocytes/metabolism , Collagen/biosynthesis , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Animals , Cartilage/metabolism , Extracellular Matrix/metabolism , Glucose/metabolism , Glutamine/metabolism , Growth Plate/metabolism , Hydroxylation , Hypoxia-Inducible Factor-Proline Dioxygenases/deficiency , Hypoxia-Inducible Factor-Proline Dioxygenases/genetics , Ketoglutaric Acids/metabolism , Lysine/metabolism , Male , Mice , Osteogenesis , Oxidation-Reduction , Proline/metabolism
8.
Liver Int ; 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38847551

ABSTRACT

BACKGROUND & AIMS: Cystic fibrosis (CF) is considered a multisystemic disorder in which CF-associated liver disease (CFLD) is the third most common cause of mortality. Currently, no effective treatment is available for CFLD because its pathophysiology is still unclear. Interestingly, CFLD exhibits identical vascular characteristics as non-cirrhotic portal hypertension, recently classified as porto-sinusoidal vascular disorders (PSVD). METHODS: Since endothelial cells (ECs) are an important component in PSVD, we performed single-cell RNA sequencing (scRNA-seq) on four explant livers from CFLD patients to identify differential endothelial characteristics which could contribute to the disease. We comprehensively characterized the endothelial compartment and compared it with publicly available scRNA-seq datasets from cirrhotic and healthy livers. Key gene signatures were validated ex vivo on patient tissues. RESULTS: We found that ECs from CF liver explants are more closely related to healthy than cirrhotic patients. In CF patients we also discovered a distinct population of liver sinusoidal ECs-coined CF LSECs-upregulating genes involved in the complement cascade and coagulation. Finally, our immunostainings further validated the predominant periportal location of CF LSECs. CONCLUSIONS: Our work showed novel aspects of human liver ECs at the single-cell level thereby supporting endothelial involvement in CFLD, and reinforcing the hypothesis that ECs could be a driver of PSVD. Therefore, considering the vascular compartment in CF and CFLD may help developing new therapeutic approaches for these diseases.

9.
Nature ; 561(7721): 63-69, 2018 09.
Article in English | MEDLINE | ID: mdl-30158707

ABSTRACT

Glutamine synthetase, encoded by the gene GLUL, is an enzyme that converts glutamate and ammonia to glutamine. It is expressed by endothelial cells, but surprisingly shows negligible glutamine-synthesizing activity in these cells at physiological glutamine levels. Here we show in mice that genetic deletion of Glul in endothelial cells impairs vessel sprouting during vascular development, whereas pharmacological blockade of glutamine synthetase suppresses angiogenesis in ocular and inflammatory skin disease while only minimally affecting healthy adult quiescent endothelial cells. This relies on the inhibition of endothelial cell migration but not proliferation. Mechanistically we show that in human umbilical vein endothelial cells GLUL knockdown reduces membrane localization and activation of the GTPase RHOJ while activating other Rho GTPases and Rho kinase, thereby inducing actin stress fibres and impeding endothelial cell motility. Inhibition of Rho kinase rescues the defect in endothelial cell migration that is induced by GLUL knockdown. Notably, glutamine synthetase palmitoylates itself and interacts with RHOJ to sustain RHOJ palmitoylation, membrane localization and activation. These findings reveal that, in addition to the known formation of glutamine, the enzyme glutamine synthetase shows unknown activity in endothelial cell migration during pathological angiogenesis through RHOJ palmitoylation.


Subject(s)
Endothelial Cells/enzymology , Endothelial Cells/pathology , Glutamate-Ammonia Ligase/metabolism , Glutamine/biosynthesis , Neovascularization, Pathologic , Actins/metabolism , Animals , Cell Movement , Endothelial Cells/metabolism , Female , Glutamate-Ammonia Ligase/deficiency , Glutamate-Ammonia Ligase/genetics , Glutamate-Ammonia Ligase/physiology , HEK293 Cells , Human Umbilical Vein Endothelial Cells/cytology , Human Umbilical Vein Endothelial Cells/enzymology , Human Umbilical Vein Endothelial Cells/metabolism , Humans , Lipoylation , Mice , Palmitic Acid/metabolism , Protein Processing, Post-Translational , Stress Fibers/metabolism , rho GTP-Binding Proteins/chemistry , rho GTP-Binding Proteins/metabolism , rho-Associated Kinases/metabolism
10.
Nature ; 542(7639): 49-54, 2017 02 02.
Article in English | MEDLINE | ID: mdl-28024299

ABSTRACT

Lymphatic vessels are lined by lymphatic endothelial cells (LECs), and are critical for health. However, the role of metabolism in lymphatic development has not yet been elucidated. Here we report that in transgenic mouse models, LEC-specific loss of CPT1A, a rate-controlling enzyme in fatty acid ß-oxidation, impairs lymphatic development. LECs use fatty acid ß-oxidation to proliferate and for epigenetic regulation of lymphatic marker expression during LEC differentiation. Mechanistically, the transcription factor PROX1 upregulates CPT1A expression, which increases acetyl coenzyme A production dependent on fatty acid ß-oxidation. Acetyl coenzyme A is used by the histone acetyltransferase p300 to acetylate histones at lymphangiogenic genes. PROX1-p300 interaction facilitates preferential histone acetylation at PROX1-target genes. Through this metabolism-dependent mechanism, PROX1 mediates epigenetic changes that promote lymphangiogenesis. Notably, blockade of CPT1 enzymes inhibits injury-induced lymphangiogenesis, and replenishing acetyl coenzyme A by supplementing acetate rescues this process in vivo.


Subject(s)
Fatty Acids/chemistry , Fatty Acids/metabolism , Lymphangiogenesis , Lymphatic Vessels/cytology , Lymphatic Vessels/metabolism , Acetates/pharmacology , Acetyl Coenzyme A/metabolism , Acetylation/drug effects , Animals , Carnitine O-Palmitoyltransferase/antagonists & inhibitors , Carnitine O-Palmitoyltransferase/genetics , Carnitine O-Palmitoyltransferase/metabolism , Cell Differentiation/drug effects , Cell Differentiation/genetics , Endothelial Cells/cytology , Endothelial Cells/drug effects , Endothelial Cells/metabolism , Epigenesis, Genetic , Female , Histones/metabolism , Homeodomain Proteins/metabolism , Human Umbilical Vein Endothelial Cells , Humans , Lymphangiogenesis/drug effects , Lymphangiogenesis/genetics , Lymphatic Vessels/drug effects , Mice , Mice, Inbred C57BL , Oxidation-Reduction/drug effects , Protein Biosynthesis , Transcription, Genetic , Tumor Suppressor Proteins/metabolism , Umbilical Arteries/cytology , Up-Regulation
12.
Acta Pharmacol Sin ; 44(3): 680-692, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36114272

ABSTRACT

The growth of solid tumors depends on tumor vascularization and the endothelial cells (ECs) that line the lumen of blood vessels. ECs generate a large fraction of ATP through glycolysis, and elevation of their glycolytic activity is associated with angiogenic behavior in solid tumors. 6-Phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) positively regulates glycolysis via fructose-2/6-bisphosphate, the product of its kinase activity. Partial inhibition of glycolysis in tumor ECs by targeting PFKFB3 normalizes the otherwise abnormal tumor vessels, thereby reducing metastasis and improving the outcome of chemotherapy. Although a limited number of tool compounds exist, orally available PFKFB3 inhibitors are unavailable. In this study we conducted a high-throughput screening campaign against the kinase activity of PFKFB3, involving 250,240 chemical compounds. A total of 507 initial hits showing >50% inhibition at 20 µM were identified, 66 of them plus 1 analog from a similarity search consistently displayed low IC50 values (<10 µM). In vitro experiments yielded 22 nontoxic hits that suppressed the tube formation of primary human umbilical vein ECs at 10 µM. Of them, 15 exhibited binding affinity to PFKFB3 in surface plasmon resonance assays, including 3 (WNN0403-E003, WNN1352-H007 and WNN1542-F004) that passed the pan-assay interference compounds screening without warning flags. This study provides potential leads to the development of new PFKFB3 inhibitors.


Subject(s)
High-Throughput Screening Assays , Neoplasms , Phosphofructokinase-2 , Humans , Glycolysis , Human Umbilical Vein Endothelial Cells/metabolism , Neoplasms/metabolism , Neovascularization, Pathologic , Phosphofructokinase-2/antagonists & inhibitors , Phosphofructokinase-2/metabolism
13.
Circ Res ; 127(2): 310-329, 2020 07 03.
Article in English | MEDLINE | ID: mdl-32833569

ABSTRACT

All organisms growing beyond the oxygen diffusion limit critically depend on a functional vasculature for survival. Yet blood vessels are far more than passive, uniform conduits for oxygen and nutrient supply. A remarkable organotypic heterogeneity is brought about by tissue-specific differentiated endothelial cells (lining the blood vessels' lumen) and allows blood vessels to deal with organ-specific demands for homeostasis. On the flip side, when blood vessels go awry, they promote life-threatening diseases characterized by endothelial cells inappropriately adopting an angiogenic state (eg, tumor vascularization) or becoming dysfunctional (eg, diabetic microvasculopathies), calling respectively for antiangiogenic therapies and proangiogenic/vascular regenerative strategies. In solid tumors, despite initial enthusiasm, growth factor-based (mostly anti-VEGF [vascular endothelial growth factor]) antiangiogenic therapies do not sufficiently live up to the expectations in terms of efficiency and patient survival, in part, due to intrinsic and acquired therapy resistance. Tumors cunningly deploy alternative growth factors than the ones targeted by the antiangiogenic therapies to reinstigate angiogenesis or revert to other ways of securing blood flow, independently of the targeted growth factors. In trying to alleviate tissue ischemia and to repair dysfunctional or damaged endothelium, local in-tissue administration of (genes encoding) proangiogenic factors or endothelial (stem) cells harnessing regenerative potential have been explored. Notwithstanding evaluation in clinical trials, these approaches are often hampered by dosing issues and limited half-life or local retention of the administered agents. Here, without intending to provide an all-encompassing historical overview, we focus on some recent advances in understanding endothelial cell behavior in health and disease and identify novel molecular players and concepts that could eventually be considered for therapeutic targeting.


Subject(s)
Neovascularization, Pathologic/metabolism , Neovascularization, Physiologic , Animals , Blood Vessels/cytology , Blood Vessels/metabolism , Blood Vessels/physiology , Humans , Neovascularization, Pathologic/pathology , Neovascularization, Pathologic/therapy , Regeneration
14.
Nature ; 529(7585): 216-20, 2016 Jan 14.
Article in English | MEDLINE | ID: mdl-26735015

ABSTRACT

Endothelial cells (ECs) are plastic cells that can switch between growth states with different bioenergetic and biosynthetic requirements. Although quiescent in most healthy tissues, ECs divide and migrate rapidly upon proangiogenic stimulation. Adjusting endothelial metabolism to the growth state is central to normal vessel growth and function, yet it is poorly understood at the molecular level. Here we report that the forkhead box O (FOXO) transcription factor FOXO1 is an essential regulator of vascular growth that couples metabolic and proliferative activities in ECs. Endothelial-restricted deletion of FOXO1 in mice induces a profound increase in EC proliferation that interferes with coordinated sprouting, thereby causing hyperplasia and vessel enlargement. Conversely, forced expression of FOXO1 restricts vascular expansion and leads to vessel thinning and hypobranching. We find that FOXO1 acts as a gatekeeper of endothelial quiescence, which decelerates metabolic activity by reducing glycolysis and mitochondrial respiration. Mechanistically, FOXO1 suppresses signalling by MYC (also known as c-MYC), a powerful driver of anabolic metabolism and growth. MYC ablation impairs glycolysis, mitochondrial function and proliferation of ECs while its EC-specific overexpression fuels these processes. Moreover, restoration of MYC signalling in FOXO1-overexpressing endothelium normalizes metabolic activity and branching behaviour. Our findings identify FOXO1 as a critical rheostat of vascular expansion and define the FOXO1-MYC transcriptional network as a novel metabolic checkpoint during endothelial growth and proliferation.


Subject(s)
Endothelium, Vascular/growth & development , Endothelium, Vascular/metabolism , Forkhead Transcription Factors/metabolism , Animals , Cell Proliferation , Cell Respiration , Endothelium, Vascular/cytology , Female , Forkhead Box Protein O1 , Forkhead Transcription Factors/deficiency , Forkhead Transcription Factors/genetics , Glycolysis , Human Umbilical Vein Endothelial Cells/cytology , Human Umbilical Vein Endothelial Cells/metabolism , Humans , Male , Mice , Mice, Inbred C57BL , Proto-Oncogene Proteins c-myc/deficiency , Proto-Oncogene Proteins c-myc/genetics , Proto-Oncogene Proteins c-myc/metabolism , Signal Transduction
15.
Nucleic Acids Res ; 48(W1): W385-W394, 2020 07 02.
Article in English | MEDLINE | ID: mdl-32392297

ABSTRACT

The amount of biological data, generated with (single cell) omics technologies, is rapidly increasing, thereby exacerbating bottlenecks in the data analysis and interpretation of omics experiments. Data mining platforms that facilitate non-bioinformatician experimental scientists to analyze a wide range of experimental designs and data types can alleviate such bottlenecks, aiding in the exploration of (newly generated or publicly available) omics datasets. Here, we present BIOMEX, a browser-based software, designed to facilitate the Biological Interpretation Of Multi-omics EXperiments by bench scientists. BIOMEX integrates state-of-the-art statistical tools and field-tested algorithms into a flexible but well-defined workflow that accommodates metabolomics, transcriptomics, proteomics, mass cytometry and single cell data from different platforms and organisms. The BIOMEX workflow is accompanied by a manual and video tutorials that provide the necessary background to navigate the interface and get acquainted with the employed methods. BIOMEX guides the user through omics-tailored analyses, such as data pretreatment and normalization, dimensionality reduction, differential and enrichment analysis, pathway mapping, clustering, marker analysis, trajectory inference, meta-analysis and others. BIOMEX is fully interactive, allowing users to easily change parameters and generate customized plots exportable as high-quality publication-ready figures. BIOMEX is open source and freely available at https://www.vibcancer.be/software-tools/biomex.


Subject(s)
Gene Expression Profiling/methods , Single-Cell Analysis/methods , Software , Algorithms , Bile Duct Neoplasms/genetics , Cholangiocarcinoma/genetics , Computer Graphics , Endothelial Cells/metabolism , Humans , Metabolomics/methods , Neoplasms/mortality , Proteomics/methods , Survival Analysis , Workflow
16.
EMBO J ; 36(16): 2334-2352, 2017 08 15.
Article in English | MEDLINE | ID: mdl-28659375

ABSTRACT

Endothelial cell (EC) metabolism is emerging as a regulator of angiogenesis, but the precise role of glutamine metabolism in ECs is unknown. Here, we show that depriving ECs of glutamine or inhibiting glutaminase 1 (GLS1) caused vessel sprouting defects due to impaired proliferation and migration, and reduced pathological ocular angiogenesis. Inhibition of glutamine metabolism in ECs did not cause energy distress, but impaired tricarboxylic acid (TCA) cycle anaplerosis, macromolecule production, and redox homeostasis. Only the combination of TCA cycle replenishment plus asparagine supplementation restored the metabolic aberrations and proliferation defect caused by glutamine deprivation. Mechanistically, glutamine provided nitrogen for asparagine synthesis to sustain cellular homeostasis. While ECs can take up asparagine, silencing asparagine synthetase (ASNS, which converts glutamine-derived nitrogen and aspartate to asparagine) impaired EC sprouting even in the presence of glutamine and asparagine. Asparagine further proved crucial in glutamine-deprived ECs to restore protein synthesis, suppress ER stress, and reactivate mTOR signaling. These findings reveal a novel link between endothelial glutamine and asparagine metabolism in vessel sprouting.


Subject(s)
Asparagine/metabolism , Cell Movement/drug effects , Cell Proliferation/drug effects , Endothelial Cells/drug effects , Endothelial Cells/physiology , Glutamine/metabolism , Neovascularization, Physiologic/drug effects , Culture Media/chemistry , Endothelial Cells/metabolism , Glutaminase/metabolism , Human Umbilical Vein Endothelial Cells , Humans , Metabolic Networks and Pathways , Neovascularization, Pathologic
17.
Eur Respir J ; 57(4)2021 04.
Article in English | MEDLINE | ID: mdl-33184117

ABSTRACT

Cystic fibrosis (CF) is a life-threatening disorder characterised by decreased pulmonary mucociliary and pathogen clearance, and an exaggerated inflammatory response leading to progressive lung damage. CF is caused by bi-allelic pathogenic variants of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a chloride channel. CFTR is expressed in endothelial cells (ECs) and EC dysfunction has been reported in CF patients, but a role for this ion channel in ECs regarding CF disease progression is poorly described.We used an unbiased RNA sequencing approach in complementary models of CFTR silencing and blockade (by the CFTR inhibitor CFTRinh-172) in human ECs to characterise the changes upon CFTR impairment. Key findings were further validated in vitro and in vivo in CFTR-knockout mice and ex vivo in CF patient-derived ECs.Both models of CFTR impairment revealed that EC proliferation, migration and autophagy were downregulated. Remarkably though, defective CFTR function led to EC activation and a persisting pro-inflammatory state of the endothelium with increased leukocyte adhesion. Further validation in CFTR-knockout mice revealed enhanced leukocyte extravasation in lung and liver parenchyma associated with increased levels of EC activation markers. In addition, CF patient-derived ECs displayed increased EC activation markers and leukocyte adhesion, which was partially rescued by the CFTR modulators VX-770 and VX-809.Our integrated analysis thus suggests that ECs are no innocent bystanders in CF pathology, but rather may contribute to the exaggerated inflammatory phenotype, raising the question of whether normalisation of vascular inflammation might be a novel therapeutic strategy to ameliorate the disease severity of CF.


Subject(s)
Cystic Fibrosis Transmembrane Conductance Regulator , Cystic Fibrosis , Cystic Fibrosis/genetics , Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Cystic Fibrosis Transmembrane Conductance Regulator/metabolism , Endothelial Cells/metabolism , Humans , Phenotype , Transcriptome
18.
Nature ; 520(7546): 192-197, 2015 Apr 09.
Article in English | MEDLINE | ID: mdl-25830893

ABSTRACT

The metabolism of endothelial cells during vessel sprouting remains poorly studied. Here we report that endothelial loss of CPT1A, a rate-limiting enzyme of fatty acid oxidation (FAO), causes vascular sprouting defects due to impaired proliferation, not migration, of human and murine endothelial cells. Reduction of FAO in endothelial cells did not cause energy depletion or disturb redox homeostasis, but impaired de novo nucleotide synthesis for DNA replication. Isotope labelling studies in control endothelial cells showed that fatty acid carbons substantially replenished the Krebs cycle, and were incorporated into aspartate (a nucleotide precursor), uridine monophosphate (a precursor of pyrimidine nucleoside triphosphates) and DNA. CPT1A silencing reduced these processes and depleted endothelial cell stores of aspartate and deoxyribonucleoside triphosphates. Acetate (metabolized to acetyl-CoA, thereby substituting for the depleted FAO-derived acetyl-CoA) or a nucleoside mix rescued the phenotype of CPT1A-silenced endothelial cells. Finally, CPT1 blockade inhibited pathological ocular angiogenesis in mice, suggesting a novel strategy for blocking angiogenesis.


Subject(s)
Carbon/metabolism , Endothelial Cells/metabolism , Fatty Acids/chemistry , Fatty Acids/metabolism , Nucleotides/biosynthesis , Acetic Acid/pharmacology , Adenosine Triphosphate/metabolism , Animals , Blood Vessels/cytology , Blood Vessels/drug effects , Blood Vessels/metabolism , Blood Vessels/pathology , Carnitine O-Palmitoyltransferase/antagonists & inhibitors , Carnitine O-Palmitoyltransferase/deficiency , Carnitine O-Palmitoyltransferase/genetics , Carnitine O-Palmitoyltransferase/metabolism , Cell Line, Tumor , Cell Proliferation/drug effects , Citric Acid Cycle , DNA/biosynthesis , Disease Models, Animal , Endothelial Cells/cytology , Endothelial Cells/drug effects , Endothelial Cells/enzymology , Gene Silencing , Glucose/metabolism , Human Umbilical Vein Endothelial Cells/cytology , Human Umbilical Vein Endothelial Cells/drug effects , Human Umbilical Vein Endothelial Cells/metabolism , Human Umbilical Vein Endothelial Cells/pathology , Humans , Mice , Neovascularization, Pathologic/drug therapy , Neovascularization, Pathologic/metabolism , Neovascularization, Pathologic/pathology , Nucleotides/chemistry , Nucleotides/pharmacology , Oxidation-Reduction/drug effects , Retinopathy of Prematurity/drug therapy , Retinopathy of Prematurity/metabolism , Retinopathy of Prematurity/pathology
19.
Nucleic Acids Res ; 47(D1): D736-D744, 2019 01 08.
Article in English | MEDLINE | ID: mdl-30357379

ABSTRACT

Endothelial cells (ECs) line blood vessels, regulate homeostatic processes (blood flow, immune cell trafficking), but are also involved in many prevalent diseases. The increasing use of high-throughput technologies such as gene expression microarrays and (single cell) RNA sequencing generated a wealth of data on the molecular basis of EC (dys-)function. Extracting biological insight from these datasets is challenging for scientists who are not proficient in bioinformatics. To facilitate the re-use of publicly available EC transcriptomics data, we developed the endothelial database EndoDB, a web-accessible collection of expert curated, quality assured and pre-analyzed data collected from 360 datasets comprising a total of 4741 bulk and 5847 single cell endothelial transcriptomes from six different organisms. Unlike other added-value databases, EndoDB allows to easily retrieve and explore data of specific studies, determine under which conditions genes and pathways of interest are deregulated and assess reprogramming of metabolism via principal component analysis, differential gene expression analysis, gene set enrichment analysis, heatmaps and metabolic and transcription factor analysis, while single cell data are visualized as gene expression color-coded t-SNE plots. Plots and tables in EndoDB are customizable, downloadable and interactive. EndoDB is freely available at https://vibcancer.be/software-tools/endodb, and will be updated to include new studies.


Subject(s)
Computational Biology , Databases, Genetic , Transcriptome/genetics , Animals , Endothelial Cells/metabolism , Gene Expression Regulation/genetics , Humans , Principal Component Analysis
20.
J Am Soc Nephrol ; 31(1): 118-138, 2020 01.
Article in English | MEDLINE | ID: mdl-31818909

ABSTRACT

BACKGROUND: Renal endothelial cells from glomerular, cortical, and medullary kidney compartments are exposed to different microenvironmental conditions and support specific kidney processes. However, the heterogeneous phenotypes of these cells remain incompletely inventoried. Osmotic homeostasis is vitally important for regulating cell volume and function, and in mammals, osmotic equilibrium is regulated through the countercurrent system in the renal medulla, where water exchange through endothelium occurs against an osmotic pressure gradient. Dehydration exposes medullary renal endothelial cells to extreme hyperosmolarity, and how these cells adapt to and survive in this hypertonic milieu is unknown. METHODS: We inventoried renal endothelial cell heterogeneity by single-cell RNA sequencing >40,000 mouse renal endothelial cells, and studied transcriptome changes during osmotic adaptation upon water deprivation. We validated our findings by immunostaining and functionally by targeting oxidative phosphorylation in a hyperosmolarity model in vitro and in dehydrated mice in vivo. RESULTS: We identified 24 renal endothelial cell phenotypes (of which eight were novel), highlighting extensive heterogeneity of these cells between and within the cortex, glomeruli, and medulla. In response to dehydration and hypertonicity, medullary renal endothelial cells upregulated the expression of genes involved in the hypoxia response, glycolysis, and-surprisingly-oxidative phosphorylation. Endothelial cells increased oxygen consumption when exposed to hyperosmolarity, whereas blocking oxidative phosphorylation compromised endothelial cell viability during hyperosmotic stress and impaired urine concentration during dehydration. CONCLUSIONS: This study provides a high-resolution atlas of the renal endothelium and highlights extensive renal endothelial cell phenotypic heterogeneity, as well as a previously unrecognized role of oxidative phosphorylation in the metabolic adaptation of medullary renal endothelial cells to water deprivation.


Subject(s)
Adaptation, Physiological/genetics , Endothelial Cells/metabolism , Kidney/cytology , Sequence Analysis, RNA , Water Deprivation/physiology , Animals , Endothelial Cells/physiology , Male , Mice , Mice, Inbred C57BL , Phenotype
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