Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The effect of colorectal cancer (CRC) organoid-derived extracellular vesicles on the expression profile of fibroblasts

ABSTRACT: Extracellular vesicles (EV) are membrane-surrounded vesicles secreted by cells that carry biologically important molecules to the target cells. EVs form a heterogenous group and they represent a novel way of intercellular communication. To study the importance of colorectal cancer (CRC)-derived EVs on stromal fibroblasts, we applied CRC patient-derived 3D organoid cultures and commercially available human colon fibroblasts. We studied the gene expression changes in fibroblasts in the presence and absence pf CRC-derived EVs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE114979 | GEO | 2019/02/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Effects of (−)-Epigallocatechin-3-O-gallate (EGCG) on miRNAs’ expression in extracellular vesicles (EVs) derived from human umbilical vein endothelial cells (HUVECs)

Project description:EGCG, one of the major catechins in green tea, exerts an antifibrotic property, although its mechanism remains unclear. Recently, it has been reported that microRNA (miRNA) transported by extracellular vesicles (EVs) from vascular endothelial cells (VECs) are involved in PF. In this study, we assessed the effects of EGCG on miRNAs’ expression in EVs derived from HUVECs.

2023-02-15 | GSE217849 | GEO

Questioning the purity of the media - Extracellular small non-coding RNA contaminants in fetal bovine serum and serum-free media

Project description:In the research field of extracellular vesicles (EVs), the use of EV-depleted fetal bovine serum (FBS) for in vitro studies is highly recommended to eliminate the confounding effects of media derived EVs. EV-depleted FBS may either be prepared by ultracentrifugation or bought commercially, nevertheless these depletion methods do not guarantee an RNA-free preparation. In this study we have addressed the RNA contamination issue in FBS, ultracentrifuged EV-depleted FBS, commercially available EV-depleted FBS, and also from our recently developed filtration based EV depleted FBS. Commercially available serum-free, xeno-free defined media were also screened for RNA contamination.

2019-04-30 | GSE120594 | GEO

The human pericardial fluid is enriched with cardiovascular-expressed microRNAs

Project description:The pericardial fluid (PF) surrounds the heart and it is contained in the pericardial sac. PF contains myocardial-derived factors. MicroRNAs (miRNAs) are negative post-transcriptional regulators of their target genes and they can be released into extracellular vesicles (EVs) contributing to cell-to-cell communication. We hypothesize that the PF contains miRNAs of myocardial origin and that represents a niche for the exchange of miRNAs between heart cells. In order to investigate whether PF contains functionally active miRNAs, miRNA expression profiles on PF samples collected from three patients undergoing aortic valve replacement (AVR) surgery performed during cardiopulmonary-bypass (CPB), were genereted.

2017-06-10 | GSE80577 | GEO

Melanoma-derived extracellular vesicles mediate lymphatic remodeling and impair tumor immunity in draining lymph nodes

Project description:Transcriptional comparison of B16F10 cells with B16F10 cell-derived extracellular vesicles (EVs) to identify transcripts enriched or de-enriched in EVs compared to their donor cells.

2022-03-01 | E-MTAB-11025 | biostudies-arrayexpress

The transcriptome profile of the stomach fibroblasts with high-metastatic or low-metastatic gastric cancer cell-derived extracellular vesicles.

Project description:Cancer-associated fibroblasts (CAFs) have an important role in the tumor progression. CAFs are heterogeneous, and its subpopulation with distinct functions have been regarded as the major obstacle to CAF targeting therapy. However, it is still unclear how cancer cells mediate CAF subpopulations and create preferable tumor microenvironment for their metastasis. In this study, by using the metastatic cancer cell line models of diffuse-type gastric cancer (DGC), we demonstrate that high-metastatic cancer cell-derived extracellular vesicles (EVs) contribute to the formation of activated fibroblast subpopulations. High-metastatic DGC cells create at least two types of CAF subpopulations: myofibroblastic feature and chemokine producing feature. The CAF subpopulation with chemokine producing feature was selectively induced by high-metastatic DGC cell-derived EVs. We also found that high-metastatic DGC cell-derived EVs contain various miRNAs to induce chemokine expression in the fibroblasts. Our findings suggest that intercellular communications via EVs contribute to establishing the appropriate tumor microenvironment toward cancer metastasis. To study the effect of EVs derived from GC cell lines on gene expression in the stomach fibroblasts, transcriptome analysis for the stomach fibroblasts with EVs derived from GC cell lines was performed.

2019-03-31 | GSE116176 | GEO

The effect of colorectal cancer (CRC) organoid-derived extracellular vesicles on the expression profile of fibroblasts

Project description:The effect of colorectal cancer (CRC) organoid-derived extracellular vesicles on the expression profile of fibroblasts

| PRJNA473425 | ENA

The profile of miRNAs in extracellular vesicles derived from high-metastatic or low-metastatic gastric cancer cell lines.

Project description:Cancer-associated fibroblasts (CAFs) have an important role in the tumor progression. CAFs are heterogeneous, and its subpopulation with distinct functions have been regarded as the major obstacle to CAF targeting therapy. However, it is still unclear how cancer cells mediate CAF subpopulations and create preferable tumor microenvironment for their metastasis. In this study, by using the metastatic cancer cell line models of diffuse-type gastric cancer (DGC), we demonstrate that high-metastatic cancer cell-derived extracellular vesicles (EVs) contribute to the formation of activated fibroblast subpopulations. High-metastatic DGC cells create at least two types of CAF subpopulations: myofibroblastic feature and chemokine producing feature. The CAF subpopulation with chemokine producing feature was selectively induced by high-metastatic DGC cell-derived EVs. We also found that high-metastatic DGC cell-derived EVs contain various miRNAs to induce chemokine expression in the fibroblasts. Our findings suggest that intercellular communications via EVs contribute to establishing the appropriate tumor microenvironment toward cancer metastasis.To ask how high-metastatic DGC cell-derived EVs induced chemokines in the stomach fibroblasts, miRNA microarray analysis of DGC cell-derived EVs was performed.

2019-03-31 | GSE116143 | GEO

Crosstalk between the effects of extracellular vesicles (Evs) and TNF on U937 human monocyte cell line

Project description:Under physiological conditions, extracellular vesicles (EVs) are present simultaneously in the extracellular compartment together with cytokines. Thus, we hypothesized that EVs in combination with cytokines induce different responses of monocyte cells compared to EVs or cytokines alone. Human monocyte U937 cells were incubated with EV-containing or EV-free CCRF human T-cell supernatant, with or without the addition of TNF. U937 cells cultured in EV-free supernatant, supernatant containing CCRF t-cell derived EVs, TNF or both. Each treatment option was measured in 3 replicates.

2013-06-19 | E-GEOD-47897 | biostudies-arrayexpress

Growth media conditions influence the secretion route and release levels of engineered extracellular vesicles

Project description:Extracellular vesicles (EVs) are nanosized cell-derived vesicles found in all bodily fluids which provide a route of intercellular communication by transmitting biological cargo. While EVs offer promise as therapeutic agents, the molecular mechanisms of EV biogenesis are not yet fully elucidated, in part due to the concurrence of numerous interwoven pathways which give rise to heterogenous EV populations in vitro. The effects of conditions in the cellular environment on EV production are of particular interest. In this study, we utilize a quantifiable EV-engineering approach to investigate how various cell media conditions alter EV production. The presence of serum, exogenous EVs, and other signaling factors in cell media alters EV production on physical, molecular, and transcriptional levels. Further, we demonstrate that exosome biogenesis pathways are the major factors contributing to EV production under optimized conditions. Our findings suggest a novel understanding to the mechanisms underlying EV production in cell culture which can be applied to develop advanced EV production methods.

2021-04-29 | GSE173474 | GEO

CELL-EXO_01

Project description:In this study, we address mRNA composition of hepatocyte-like derived extracellular vesicles (EVs), using as cellular model the mouse liver derived cell line MLP29, and primary cell culture of rat hepatocyte (RH) obtained by in vivo liver perfusion. The study shows qualitative characterization of RNA, identification of transcripts and its functional characterization through gene expression array technique. To reach a deeper nowledge in the biology of EVs, we perform RNase protection assay, density gradients matching RNA with typical exosomal protein markers, and capture assays to probe that mRNA was internalized. Aim of the project: To identify transcripts present in extracellular vesicles secreted by Rat hepatocytes primary cell culture and to identify extracellular vesicles secreted by mouse hepatocyte cell line MLP29, and in this case, compare the enrichment of transcripts respect to the cell, to know if the composition in the extracellular vesicles is similar to the cell, or if their composition is not directly determined by the abundance of transcripts in the cell.

2013-07-23 | E-MEXP-3740 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data