ScRNAseq atlas of mouse bone marrow endothelial cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB76309 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13766043.fastq.gz | Fastqsanger.gz | |||
| ERR13766054.fastq.gz | Fastqsanger.gz | |||
| ERR13765359.fastq.gz | Fastqsanger.gz | |||
| ERR13765360.fastq.gz | Fastqsanger.gz | |||
| ERR13763483.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Although endothelial cells (ECs) have been shown to contribute to HSC maintenance in bone marrow (BM), differential contributions of EC subtypes remain unknown, owing to the lack of methods to separate with high purity arterial (AEC) from sinusoidal (SEC) endothelial cells. We show that combination of podoplanin (PDPN) and Sca-1 expression distinguishes AEC from SEC where Sca1brightPDPN—CD45—Ter119— cells exhibit an arterial gene signature and PDPN+Sca1dimCD45—Ter119— marks sinusoids. PDPN can be substituted for antibodies against the adhesion molecules ICAM1 or E-selectin that also mark SEC. We performed functional analysis of these different types of endothelial cells and found that SCF secreated from AECs regulate HSCs.
2018-06-27 | GSE104701 | GEO
Project description:To determine a gene/molecular fingerprint of multiple myeloma (MM) endothelial cells (MMECs), also identifying some of the vascular mechanisms that govern the malignant progression from quiescent monoclonal gammopathy of undetermined significance (MGUS). A comparative gene expression profiling (GEP) was carried out on patient-derived MMECs and MGUS endothelial cells (MGECs) using the Affymetrix U133A Arrays. Expression of selective vascular markers were also validated by RT-PCR and immunoblotting analysis in primary cultures of ECs isolated from total bone marrow (BM)-mononuclear cells. Twenty-two genes were found differently expressed in MMECs compared to MGECs (with 14 down-regulated and 8 up-regulated), thus proving that molecular differences were maintained in vitro. Specific pathways analysis revealed transcriptional and protein expression changes for key regulators of extracellular matrix formation and bone remodeling, cell-adhesion, chemotaxis, angiogenesis, resistance to apoptosis, and cell-cycle regulation. Specifically, we focused on six of these genes (DIRAS3, SERPINF1, SRPX, BNIP3, IER3 and SEPW1), which were not previously functionally correlated to the overangiogenic phenotype of MMECs and disease activity. These data identified distinct EC gene expression profiles and some vascular phenotypes that could influence the remodeling of the BM-microenvironment in patients with active MM. A better understanding of the linkage between genetic and epigenetic events in MM tumor/ECs may contribute to the molecular classification of the disease, thereby identifying selective targets of more effective anti-vessel/stroma therapeutic strategies. Keywords: Gene expression profiling, endothelial cells, Multiple Myeloma.
2009-08-31 | GSE14230 | GEO
Project description:To determine a gene/molecular fingerprint of multiple myeloma (MM) endothelial cells (MMECs), also identifying some of the vascular mechanisms that govern the malignant progression from quiescent monoclonal gammopathy of undetermined significance (MGUS). A comparative gene expression profiling (GEP) was carried out on patient-derived MMECs and MGUS endothelial cells (MGECs) using the Affymetrix U133A Arrays. Expression of selective vascular markers were also validated by RT-PCR and immunoblotting analysis in primary cultures of ECs isolated from total bone marrow (BM)-mononuclear cells. Twenty-two genes were found differently expressed in MMECs compared to MGECs (with 14 down-regulated and 8 up-regulated), thus proving that molecular differences were maintained in vitro. Specific pathways analysis revealed transcriptional and protein expression changes for key regulators of extracellular matrix formation and bone remodeling, cell-adhesion, chemotaxis, angiogenesis, resistance to apoptosis, and cell-cycle regulation. Specifically, we focused on six of these genes (DIRAS3, SERPINF1, SRPX, BNIP3, IER3 and SEPW1), which were not previously functionally correlated to the overangiogenic phenotype of MMECs and disease activity. These data identified distinct EC gene expression profiles and some vascular phenotypes that could influence the remodeling of the BM-microenvironment in patients with active MM. A better understanding of the linkage between genetic and epigenetic events in MM tumor/ECs may contribute to the molecular classification of the disease, thereby identifying selective targets of more effective anti-vessel/stroma therapeutic strategies. Experiment Overall Design: This series of microarray experiments contains the gene expression profiles of five samples from HUVECs (Human Umbilical Vein Endothelial Cells) and five bone marrow ECs (endothelial cells) samples from newly diagnosed MGUS and MM patients, respectively. Centrifugation on Ficoll gradient of heparinized BM-aspirates was followed by polystyrene flask adherence to isolate stromal cells from plasma cells in suspension. Adherent stromal elements were first immunodepleted of macrophages and residual plasma cells with CD14 and CD38 monoclonal antibody (mAb)-coated flasks (mAbs were from Immunotech, Coulter, Marseilles, France), and then incubated with magnetic microbeads coated with Ulex europaeus-1 lectin. Freshly-isolated ECs were cultured in complete medium RPMI-1640 medium supplemented with 10% heat-inactivated FCS and 1% glutamine to allow cell spreading and growth. The purity and viability of EC cultures grown at least one passage (more than 97% viable cells) were assessed by fluorescence-activated cell sorting (FACS, FACS Canto II, Becton Dickinson, San Jose, CA) with double positivity for factor VIII-related antigen (FVIII-RA, a highly specific EC marker) and CD105 (or endoglyn, a molecule strongly expressed by ECs) as well as for CD14 and CD38 negativity. Analysis of mRNA transcripts for FVIII-RA, CD38, CD105 and IgH VDJ region was also performed by RT-PCR, and EC viability was assessed by trypan blue viable staining. HUVECs were purchased from Clonetics Biowhittaker (Walkersville, MD) and cultured in EGM-2MV media (Clonetics Biowhittaker). Five micrograms of total RNA was processed and, in accordance with the manufacturer's protocols, 15 micrograms of fragmented biotin-labelled cRNA were hybridized on GeneChip Human Genome U133A Arrays (Affymetrix Inc.). The arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix). The images were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software and the probe level data converted to expression values using the Bioconductor function for the Robust Multi-Array average (RMA) procedure (Irizarry et al, 2003), in which perfect match intensities are background adjusted, quantile-quantile normalized and log2-transformed.
2009-09-15 | E-GEOD-14230 | biostudies-arrayexpress
Project description:To delineate the potential molecular mechanisms underlying the communication between neutrophils and NK cells, we performed scRNAseq of the neutropenic bone marrow (12 months after transplantation of Cebpacre/+ Sbds +/+ or F/F cells). To this end, bone marrow cells were subsorted into HSC+MPP (LKS CD48-), HPC1 (LKS CD48+CD150-), B and T cells (B220+, CD3+), NK cells (NK1.1+ NKp46+) and a myeloid ‘rest’ fraction (B220-,CD3-,NKp46- and NK1.1-) and sorted fractions pooled together to obtain robust representation of all bone marrow cell types in the scRNAseq data
2022-12-31 | E-MTAB-12428 | biostudies-arrayexpress
Project description:Macrophage colony stimulating factor-1 (CSF-1) plays a critical role in maintaining myeloid lineage cells. However, congenital global deficiency of CSF-1 (Csf1op/op) causes severe musculoskeletal defects that may indirectly affect hematopoiesis. Indeed, we show here that osteolineage-derived Csf1 prevented developmental abnormalities but had no effect on monopoiesis in adulthood. However, ubiquitous deletion of Csf1 conditionally in adulthood decreased monocyte survival, differentiation, and migration, independent of its effects on bone development. Bone histology revealed that monocytes reside near sinusoidal endothelial cells (ECs) and leptin receptor (Lepr)-expressing perivascular mesenchymal stromal cells (MSCs). Targeted deletion of Csf1 from sinusoidal ECs selectively reduced Ly6C- monocytes, whereas combined depletion of Csf1 from ECs and MSCs further decreased Ly6Chi cells. Moreover, EC-derived CSF-1 facilitated recovery of Ly6C- monocytes and protected mice from weight loss following induction of polymicrobial sepsis. Thus, monocytes are supported by distinct cellular sources of CSF-1 within a perivascular BM niche.
2022-05-03 | GSE201162 | GEO
Project description:The heterogeneity of endothelial cells (ECs), lining blood vessels, across tissues remains incompletely inventoried. We constructed an atlas of >32,000 single-EC transcriptomic data from 11 tissues of the model organism Mus musculus. We propose a new classification of EC phenotypes based on transcriptome signatures and inferred putative biological features. We identified top-ranking markers for ECs from each tissue. ECs from different vascular beds (arteries, capillaries, veins, lymphatics) resembled each other across tissues, but only arterial, venous and lymphatic (not capillary) ECs shared markers, illustrating a greater heterogeneity of capillary ECs. We identified high-endothelial-venule and lacteal-like ECs in the intestines, and angiogenic ECs in healthy tissues. Metabolic transcriptomes of ECs differed amongst spleen, lung, liver, brain and testis, while being similar for kidney, heart, muscle and intestines. Within tissues, metabolic gene expression was heterogeneous amongst ECs from different vascular beds, altogether highlighting large EC heterogeneity.
2020-02-13 | E-MTAB-8077 | biostudies-arrayexpress
Project description:Native bone marrow mesenchymal stem/stromal cells (BM-MSCs) participate in generating and shaping the skeleton and bone marrow throughout the lifespan. Moreover, BM-MSCs regulate hematopoiesis by contributing to the hematopoietic stem cell niche in providing critical cytokines, chemokines and extracellular matrix components. However, BM-MSCs per se contain a heterogeneous cell population that remains ill-defined. Although studies on the taxonomy of native BM-MSCs in mice have just started to emerge, the taxonomy of native human BM-MSCs remains unelucidated. By using single-cell RNA sequencing (scRNA-seq), we aimed to define a proper taxonomy for native human BM non-hematopoietic subsets including endothelial cells (ECs) and mural cells (MCs) but with a focal point on MSCs. To this end, transcriptomic scRNA-seq data were generated from 5 distinct BM donors and were analyzed together with other transcriptomic data and with bioinformatics analyses at different levels to identify, characterize and classify distinct native subsets with relevant biomarkers. We could ascribe novel specific biomarkers to ECs, MCs and MSCs. Unlike ECs and MCs, MSCs exhibited an adipogenic transcriptomic pattern while co-expressing genes related to hematopoiesis support and multilineage commitment potential. Furthermore, by a comparative analysis of scRNA-seq of BM cells from humans and mice, we identified core genes conserved in both species. Notably, we identified MARCKS, CXCL12, PDGFRA, and LEPR together with adipogenic factors as archetypal biomarkers to reveal native MSCs within BM. In addition, our data suggest some complex gene nodes regulating critical biological functions of native BM-MSCs together with a preferential commitment toward an adipocyte lineage. Overall, our taxonomy for native BM non-hematopoietic compartment provides an explicit depiction of gene expression in human ECs, MCs and MSCs at single-cell resolution. This analysis helps enhance our understanding of the phenotype and the complexity of biological functions of native human BM-MSCs.
2023-07-26 | GSE224152 | GEO
Project description:Conflicting reports exist on whether endothelial cells (ECs) serve as a source of bone marrow stromal cells (BMSCs). In studies concerning the endothelial-to-mesenchymal transition (EndoMT), ECs expressing mesenchymal markers, as well as BMSCs expressing endothelial markers, are typically considered intermediates of EndoMT. To understand the lineage relationship between ECs and BMSCs in postnatal mouse bone marrow, we performed single-cell RNA sequencing (scRNA-seq) on ECs and BMSCs obtained from 5-week-old wild-type C57BL/6J mice, and analyzed the potential intermediates of EndoMT. Subsequently, BMSC and EC lineage tracing models, flow cytometry, and immunostaining techniques were used to validate the findings from scRNA-seq analysis.
2023-11-24 | GSE168333 | GEO
Project description:Angiogenesis is essential for cyclic endometrial growth, implantation, and pregnancy maintenance. Vasculogenesis, the formation of new blood vessels by bone marrow (BM)-derived endothelial progenitor cells (EPCs), has been shown to contribute to endometrial vasculature. However, it is unknown whether vasculogenesis occurs in neovascularization of the decidua during pregnancy. To investigate the contribution of BM-derived EPCs to vascularization of the pregnant uterus, we induced non-gonadotoxic submyeloablation by 5-fluorouracil administration to wild-type FVB/N female mice recipients followed by BM transplantation from transgenic mice expressing green fluorescent protein (GFP) under regulation of Tie2 endothelial-specific promoter. Following 1 month, Tie2-GFP BM-transplanted mice were bred and sacrificed at various gestational days (ED6.5, ED10.5, ED13.5, ED18.5, and postpartum). Bone-marrow-transplanted non-pregnant and saline-injected pregnant mice served as controls (n = 5-6/group). Implantation sites were analyzed by flow cytometry, immunohistochemistry, and immunofluorescence. While no GFP-positive EPCs were found in non-pregnant or early pregnant uteri of BM-transplanted mice, GFP-positive EPCs were first detected in pregnant uterus on ED10.5 (0.12%) and increased as the pregnancy progressed (1.14% on ED13.5), peaking on ED18.5 (1.42%) followed by decrease in the postpartum (0.9%). The percentage of endothelial cells that were BM-derived out of the total endothelial cell population in the implantation sites (GFP+CD31+/CD31+) were 9.3%, 15.8%, and 6.1% on ED13.5, ED18.5, and postpartum, respectively. Immunohistochemistry demonstrated that EPCs incorporated into decidual vasculature, and immunofluorescence showed that GFP-positive EPCs colocalized with CD31 in vascular endothelium of uterine implantation sites, confirming their endothelial lineage. Our findings indicate that BM-derived EPCs contribute to vasculogenesis of the pregnant mouse decidua.
| S-EPMC6497522 | biostudies-literature
Project description:Numerous endothelial progenitor cell (EPC)-related investigations have been performed in mouse experiments. However, defined characteristics of mouse cultured EPC have not been examined. We focused on fast versus slow adherent cell population in bone marrow mononuclear cells (BMMNCs) in culture and examined their characteristics. After 24 h-culture of BMMNCs, attached (AT) cells and floating (FL) cells were further cultured in endothelial differentiation medium separately. Immunological and molecular analyses exhibited more endothelial-like and less monocyte/macrophage-like characteristics in FL cells compared with AT cells. FL cells formed thick/stable tube and hypoxia or shear stress overload further enhanced these endothelial-like features with increased angiogenic cytokine/growth factor mRNA expressions. Finally, FL cells exhibited therapeutic potential in a mouse myocardial infarction model showing the specific local recruitment to ischemic border zone and tissue preservation. These findings suggest that slow adherent (FL) but not fast attached (AT) BMMNCs in culture are EPC-rich population in mouse.
| S-EPMC3247221 | biostudies-literature