Total RNA from EPC derived microvescicles
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE7019 | GEO | 2007/06/06
SECONDARY ACCESSION(S): PRJNA98365
REPOSITORIES: GEO
Similar Datasets
Project description:Genome -wide analysis of EPC subtypes obtained from both umbilical cord and peripheral blood. This experiment sought to compare the expression levels of eEPCs and OECs against monocytes and human dermal microvascular cells (HDMECs) in order to establish if these cells are linked to a monocytic or endothelial lineage. This is very important as the term EPC is currently used to describe cell populations which are quite dissimilar in terms of biological properties.
2010-03-01 | GSE20283 | GEO
Project description:Background: In recent times a subset of bone marrow (BM) derived cells; endothelial progenitor cells (EPCs), have generated tremendous interest, as these cells are suggested to home to sites of neovascularization and neoendothelialization and differentiate into mature endothelial cells (ECs), a process referred to as postnatal vasculogenesis. EPCs are being considered as a potential regenerative tool for treating various pathophysiological disease states including cardiovascular disorder and as a possible target to restrict vessel growth in tumour pathology. However, conflicting results have been reported in the field due to lack of EPC specific biomarkers, and the identification, characterization, and the precise role of EPCs in vascular biology still remains a subject of great debate. Therefore, the objective of this study was to use a bioinformatics approach to identify putative novel EPC specific biomarkers. Methods: This study reports a detailed gene expression profile of human umbilical cord blood (UCB) derived non-adherent CD133 + cells at different time points during in vitro differentiation (day 4 and day 7) which were compared with differentiated donor matched human umbilical vein endothelial cells (HUVEC). Results: EPC gene expression was profiled at both days 4 and 7, using affymetrix human 1.0ST exon arrays. Affymetrix gene expression profiling revealed significant expression changes in genes associated with stem/progenitor cell properties such as adhesion, signalling, molecular transport, cell structure organisation and growth. Conclusions: This is the first study utilizing gene expression profiling to examine non adherent CD133+ progenitor cells. Alterations in the gene expression reported in this study may be involved in the cellular processes characteristic of EPC development and differentiation.
2012-07-31 | GSE25979 | GEO
Project description:Purpose: To dissect the mechanisms of EPC-drived exosome in promoting endothelial cells reendothelialization, next-generation sequencing was used to determine exosome miRNA content and alterations in mRNA expression in HUVEC. Methods: The miRNA of EPC-drived exosomes sequencing was carried out on the HiSeq 2500 Platform (NovelBio Corp. Laboratory, Shanghai). The data analysis was carried out with the QIAseq miRNA quantification platform using unique molecular index (UMI) counts according to the manufacturer’s instructions. The mRNA analysis of three independent samples of PBS or EPC exosomes treated HUVEC was performed using the the HiSeq 2500 Platform (NovelBio Corp. Laboratory, Shanghai) following the manufacturer’s instructions. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: The 20 most highly expressed microRNAs identified in EPC exosomes s are listed in Table 1. The genes predicted to be targeted by those microRNAs most highly expressed in EPC exosomes (top 20 microRNAs comprising ~75% of all reads, Table 1) are most significantly enriched in the functional category ‘blood vessel development’within the top 10 categories. Further, endothelial-specific miR-21-5P was the most highly expressed microRNA in EPC exosomes. Conclusions:EPC exosomes promote vascular endothelial repair by delivering functional miR-21-5p.
2022-01-03 | GSE124692 | GEO
Project description:Comparison of mRNA expression in human EPC vs. HUVEC vs. human monocytes. Cell-type specific gene expression under basal cell culture conditions (no stimulation). The hybridization was performed with three samples of EPC vs. three samples of HUVEC vs. 3 samples of CD14+ monocytes. • The origin of the biological sample: Human endothelial progenitor cells (EPC): EPC were ex vivo cultivated from human peripheral blood-derived mononuclear cells (PBMC). PBMC were isolated by density gradient centrifugation from healthy human volunteers as previously described (Dimmeler et al., 2001). Pooled human umbilical vein endothelial cells (HUVEC) were purchased from Cambrex (Verviers, Belgium). CD14+ monocytes were purified from PBMC by positive selection with anti-CD14-microbeads (Miltenyi Biotec, Bergisch-Gladbach, Germany). Purity assessed by FACS analysis was greater than 95%. • Manipulation of biological samples and protocols used: for example, growth conditions, treatments, separation techniques: EPC: 8000000 PBMC/ml were plated on human fibronectin (Sigma, Taufkirchen, Germany) and maintained in endothelial basal medium (Cambrex) with EGM SingleQuots and 20% fetal calf serum (FCS). After 3 days, nonadherent cells were removed and adherent cells were incubated in fresh medium for 24 h before starting experiments. HUVEC: HUVEC were cultured in endothelial basal medium (Cambrex) supplemented with hydrocortisone, bovine brain extract, gentamicin, amphotericin B, epidermal growth factor, and 10% FCS until the third passage according to the manufacturer’s recommendations. CD14+ monocytes: No culture. • Protocol for preparing the hybridization extract: for example, the RNA or DNA extraction and purification protocol. Total RNA was extracted from EPC, HUVEC, and CD14+ monocytes using the RNeasy cleanup system (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Quantity and quality of total RNA was analyzed by the 2100 Bioanalyzer system (Agilent Technologies, Waldbronn, Germany) and agarose gel electrophoresis. • Labeling protocol(s): The detailed protocol for the sample preparation and microarray processing is available from Affymetrix (Santa Clara, CA). Briefly, 10 µg of purified total RNA was reverse transcribed by Superscript II reverse transcriptase (Life Technologies, Grand Island, NY) using T7-(dT)24 primer containing a T7 RNA polymerase promoter. After synthesis of the second complementary DNA (cDNA) strand, this product was used in an in vitro transcription reaction to generate biotinylated complementary RNA (cRNA). • The protocol and conditions used during hybridization, blocking and washing: Fifteen micrograms of fragmented, biotinylated cRNA were hybridized to a HG-U95Av2 microarray (Affymetrix Inc.) for 16 hours at 45° C with constant rotation at 60 rpm. This high-density oligonucleotide array targets 9,670 human genes as selected from the National Center for Biotechnology Information (NCBI) Gene Bank database with a total of 12,000 oligonucleotide sets. Each microarray was used to assay a single sample. After hybridization, the microarray was washed and stained on an Affymetrix fluidics station and scanned with an argon-ion confocal laser, with a 488 nm emission and detection at 570 nm. • GeneChip image analysis was performed using the Microarray Analysis Suite 5.0 (Affymetrix, Inc.). Expression data were analyzed utilizing the GeneSpring™ software version 4.2 (Silicon Genetics Inc., San Carlos, CA). Keywords: parallel sample
2004-12-09 | GSE2040 | GEO
Project description:Background: In recent times a subset of bone marrow (BM) derived cells; endothelial progenitor cells (EPCs), have generated tremendous interest, as these cells are suggested to home to sites of neovascularization and neoendothelialization and differentiate into mature endothelial cells (ECs), a process referred to as postnatal vasculogenesis. EPCs are being considered as a potential regenerative tool for treating various pathophysiological disease states including cardiovascular disorder and as a possible target to restrict vessel growth in tumour pathology. However, conflicting results have been reported in the field due to lack of EPC specific biomarkers, and the identification, characterization, and the precise role of EPCs in vascular biology still remains a subject of great debate. Therefore, the objective of this study was to use a bioinformatics approach to identify putative novel EPC specific biomarkers. Methods: This study reports a detailed gene expression profile of human umbilical cord blood (UCB) derived non-adherent CD133 + cells at different time points during in vitro differentiation (day 4 and day 7) which were compared with differentiated donor matched human umbilical vein endothelial cells (HUVEC). Results: EPC gene expression was profiled at both days 4 and 7, using affymetrix human 1.0ST exon arrays. Affymetrix gene expression profiling revealed significant expression changes in genes associated with stem/progenitor cell properties such as adhesion, signalling, molecular transport, cell structure organisation and growth. Conclusions: This is the first study utilizing gene expression profiling to examine non adherent CD133+ progenitor cells. Alterations in the gene expression reported in this study may be involved in the cellular processes characteristic of EPC development and differentiation. Gene expression profiling was performed on EPCs cultured for D4 and D7, on Affymetrix human 1.0ST exon array chips. Gene Spring (version GX11) was used to perform the gene expression analysis on three experimental groups; (a) D4 EPCs versus HUVEC; (b) D7 EPCs versus HUVEC and (c) D4 versus D7 EPCs.
2012-07-30 | E-GEOD-25979 | biostudies-arrayexpress
Project description:Comparison of mRNA expression in human EPC vs. HUVEC vs. human monocytes. Cell-type specific gene expression under basal cell culture conditions (no stimulation). The hybridization was performed with three samples of EPC vs. three samples of HUVEC vs. 3 samples of CD14+ monocytes. â?¢ The origin of the biological sample:; Human endothelial progenitor cells (EPC): EPC were ex vivo cultivated from human peripheral blood-derived mononuclear cells (PBMC). PBMC were isolated by density gradient centrifugation from healthy human volunteers as previously described (Dimmeler et al., 2001). Pooled human umbilical vein endothelial cells (HUVEC) were purchased from Cambrex (Verviers, Belgium). CD14+ monocytes were purified from PBMC by positive selection with anti-CD14-microbeads (Miltenyi Biotec, Bergisch-Gladbach, Germany). Purity assessed by FACS analysis was greater than 95%. â?¢ Manipulation of biological samples and protocols used: for example, growth conditions, treatments, separation techniques:; EPC:; 8000000 PBMC/ml were plated on human fibronectin (Sigma, Taufkirchen, Germany) and maintained in endothelial basal medium (Cambrex) with EGM SingleQuots and 20% fetal calf serum (FCS). After 3 days, nonadherent cells were removed and adherent cells were incubated in fresh medium for 24 h before starting experiments. HUVEC:; HUVEC were cultured in endothelial basal medium (Cambrex) supplemented with hydrocortisone, bovine brain extract, gentamicin, amphotericin B, epidermal growth factor, and 10% FCS until the third passage according to the manufacturerâ??s recommendations. CD14+ monocytes: No culture. â?¢ Protocol for preparing the hybridization extract: for example, the RNA or DNA extraction and purification protocol. Total RNA was extracted from EPC, HUVEC, and CD14+ monocytes using the RNeasy cleanup system (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Quantity and quality of total RNA was analyzed by the 2100 Bioanalyzer system (Agilent Technologies, Waldbronn, Germany) and agarose gel electrophoresis. â?¢ Labeling protocol(s):; The detailed protocol for the sample preparation and microarray processing is available from Affymetrix (Santa Clara, CA). Briefly, 10 µg of purified total RNA was reverse transcribed by Superscript II reverse transcriptase (Life Technologies, Grand Island, NY) using T7-(dT)24 primer containing a T7 RNA polymerase promoter. After synthesis of the second complementary DNA (cDNA) strand, this product was used in an in vitro transcription reaction to generate biotinylated complementary RNA (cRNA). â?¢ The protocol and conditions used during hybridization, blocking and washing:; Fifteen micrograms of fragmented, biotinylated cRNA were hybridized to a HG-U95Av2 microarray (Affymetrix Inc.) for 16 hours at 45° C with constant rotation at 60 rpm. This high-density oligonucleotide array targets 9,670 human genes as selected from the National Center for Biotechnology Information (NCBI) Gene Bank database with a total of 12,000 oligonucleotide sets. Each microarray was used to assay a single sample. After hybridization, the microarray was washed and stained on an Affymetrix fluidics station and scanned with an argon-ion confocal laser, with a 488 nm emission and detection at 570 nm. â?¢ GeneChip image analysis was performed using the Microarray Analysis Suite 5.0 (Affymetrix, Inc.). Expression data were analyzed utilizing the GeneSpringâ?¢ software version 4.2 (Silicon Genetics Inc., San Carlos, CA).
2008-06-11 | E-GEOD-2040 | biostudies-arrayexpress
Project description:Endothelial progenitor cells (EPCs) are circulating endothelial precursors shown to incorporate into foci of neovascularisation. Herein, we describe phenotypic characteristics of an EPC sub-type called endothelial colony-forming cells (ECFCs). Peripheral blood-isolated ECFCs expressed endothelial and progenitor surface antigens and displayed cobblestone-patterned colonies with clonal proliferative and angiogenic capacities in vitro. ECFCs demonstrated endothelial cell-like shear stress responses including cell alignment and PECAM-1 expression. Proteomic comparison with an endothelial reference population (human umbilical vein endothelial cells) confirmed a similar proteomic profile. Hierarchical clustering revealed two distinct ECFC clusters with differences in cell growth, proliferation and angiogenesis capacities. The cluster with compromised functionality was also associated with elevated blood pressure and impaired lipid profile. Our findings described an endothelial-like phenotype of blood-derived ECFCs with distinctive proteomic signatures based on cellular and clinical characteristics. ECFCs may aid in identifying novel mechanisms associated with cardiovascular disease risk and new targets to enhance angiogenesis.
2022-02-15 | PXD020677 | Pride
Project description:Colorectal cancer (CRC) is one of the common malignancies worldwide, accounting for a significant percentage of cancer mortality. Concurrent chemoradiation (CCRT) is now a standard treatment for unresectable malignancies of anorectum. To improve quality of life, CCRT is also commonly applied in treatment of lower rectal and anal canal cancer to preserve anal sphincter function. The most commonly used chemotherapeutic drugs combined with radiation as radiosensitizers is 5-fluorouracil (5-FU). Circulating endothelial progenitor cells (EPC), which contribute to the tumor vessel formation, reflect the response to chemotherapy both in animal model and clinical trial. Thus, circulating EPC can be used as a marker for optimizing and monitoring the anti-angiogenesis therapy including angiogenesis inhibitors and chemotherapy. Whether circulating EPC can be served as a marker of CCRT efficacy or not remains undetermined. Since CCRT is now a standard treatment of locally advanced and high-risk CRC, the development of a surrogate marker for monitoring CCRT response and optimize treatment intensity is very important.
In this grant we intent to monitor the levels of circulating EPC in locally advanced and high-risk CRC patients before, during and after CCRT. To further characterize the changes in function and biology of EPC caused by CCRT, a syngeneic animal model will be also used to evaluate the clonogenecity and specific gene expression of EPC in tumor-bearing mice receiving CCRT.
| 2028928 | ecrin-mdr-crc
Project description:Renal tubular epithelial cells were treated with cisplatin in presence or absence of EPC-derived EVs
2013-09-30 | E-MEXP-3981 | biostudies-arrayexpress
Project description:Gene expression profiles during the differentiation of EPCs into OECs were analyzed. Experiment Overall Design: RNA was isolated from Human cord blood derived- EPC and differentiated OEC from EPC. HG-U133A 2.0 microarray (54675 human genes; Affymetrix Santa Clara, CA, USA) was performed.
2008-10-26 | E-GEOD-12891 | biostudies-arrayexpress