Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigating the impact of the interstitial fluid flow and hypoxia interface on cancer biology using a spheroid-on-chip perfusion system

ABSTRACT: relied on two-dimensional (2D) static cultures which neglect the dynamic,three-dimensional (3D) nature of the biophysical tumour microenvironment (TME), especially the role and impact of interstitial fluid flow (IFF). To address this, we undertook a transcriptome-wide analysis of the impact of IFF-like perfusion flow using a spheroid-on-chip microfluidic platform using cell line MCF7 (pleural effusion of metastatic breast adenocarcinoma). IFF-like perfusion flow allows 3D cancer spheroids to be integrated into extracellular matrices (ECM)-like hydrogels and exposed to continuous perfusion, to mimic IFF in the TME. Importantly, we have performed these studies both in experimental (normoxia) and pathophysiological (hypoxia) oxygen conditions. Our data indicated that gene expression was altered by flow when compared to static conditions, and for the first time showed that these gene expression patterns differed in different oxygen tensions, reflecting a differential role of spheroid perfusion inIFF-like flow in tumour-relevant hypoxic conditions in the biophysical TME. We were also able to identify factors primarily linked with IFF-like conditions which are linked with prognostic value in cancer patients and therefore could correspond to a potential novel biomarker of IFF in cancer. This study therefore highlights the need to consider relevant oxygen conditions when studying the impact of flow in cancer biology, as well as demonstrating the potential of microfluidic models of flow to identify IFF-relevant tumour biomarkers.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Leo Zeef

PROVIDER: E-MTAB-14446 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell gene expression analysis of neutrophils from mouse tumors with and without microbial treatment

Project description:We conducted single-cell gene expression analysis of neutrophils from mouse tumors with and without microbial treatment to investigate neutrophil response in the tumor microenvironment (TME). Briefly, tumor-infiltrating Ly6G+CD11b+ neutrophils were isolated from unmanipulated tumors (resting), tumors treated with a vehicle control (control), and tumors treated with S. aureus bioparticles (stimulated) 24 hours after treatment. To survey the whole spectrum of the TME, we also isolated and sequenced non-neutrophil leukocytes in each sample.

2023-02-17 | E-MTAB-12642 | biostudies-arrayexpress

Effect of topographical micropatterning on human endothelial cells

Project description:Shear stress is known to regulate endothelial cell orientation along the direction of flow. We asked wither cellular patterning along, in the absence of shear could have similar biological effects as shear. We used DNA microarrays to examine the effect of cellular patterning on their transcriptome. Human microvascular endothelial cells were cultured in parallel micropatterned channels (30um wide channels, 30um apart) composed of polydimethylsiloxane, followed DNA Microarray analysis (Affymetrix 1.0 ST array)

2012-11-29 | E-GEOD-42596 | biostudies-arrayexpress

Integrative transcriptomic and proteomic analysis of osteocytic cells exposed to fluid flow reveals novel mechano-sensitive signaling pathways

Project description:Osteocytes, positioned within boneâs interstitial space, are subject to fluid flow upon whole bone loading. Such fluid flow is widely theorized to be a mechanical signal transduced by osteocytes, initiating a poorly understood cascade of signaling events mediating bone metabolism. The objective of this study was to utilize high-throughput approaches to examine the time course of flow-induced changes in osteocyte gene transcript and protein levels. Microarray analysis demonstrated fluid flow regulation of genes consistent with known anabolic loading responses, including Ptgs2, NF-ÎºB inhibitors, MAP3 kinases, and Wnt/Î²-catenin pathway signaling molecules. However, two of the most highly up-regulated gene productsâCxcl1 and Cxcl2, confirmed by qPCRâhave not previously been reported to be responsive to fluid flow. Gene ontology analysis suggested a highly significant inflammatory and immune response, with cellular functions including trafficking, cell-to-cell signaling, and tissue development. Proteomic analysis of the same samples demonstrated greatest up-regulation of the ATP-producing enzyme NDK, calcium-binding Calcyclin, and G protein-coupled receptor kinase 6. An integrative pathway analysis merging fold changes in transcript and protein levels predicted signaling nodes not directly detected at the sampled time points, including STAT3 and c-Myc. These results extend our knowledge of the osteocytic response to fluid flow, most notably up-regulation of Cxcl1 and Cxcl2 as a possible paracrine agent for osteoblastic and osteoclastic recruitment. Osteocyte-like MLO-Y4 cells were subjected to 2 hours of 10 dyn/cm2 oscillating fluid flow in parallel-plate fluid flow chambers and harvested for analysis at 0, 2, 8, and 24 hours post-flow incubation. Parallel control samples from sham treated cells were also collected at each time point.

2013-07-01 | E-GEOD-42874 | biostudies-arrayexpress

Testing the effect of fluid flow in dermal fibroblasts

Project description:All living cells are constantly exposed to a number of physical forces. The study aims to investigate the response of fibroblasts to dynamic mechanical forces.This experiment captures the expression data obtained by performing microarray based analysis on dermal fibroblasts subjected to 75 and 150 Âµl/min fluid flow rate.

2017-06-05 | E-MTAB-4905 | biostudies-arrayexpress

An integrated model system to study biofilm-associated adaptation to antimicrobials and resistance evolution in Pseudomonas aeruginosa MPAO1

Project description:Using an integrated model system for reproducible growth of biofilms, a JPIAMR-funded consortium of researchers* studied the expressed proteome of P. aeruginosa strain MPAO1 under i) planktonic growth, and ii) biofilm formation conditions. The model system included, as a first step, the sequencing and de novo assembly of the complete genome of this opportunistic human pathogen that belongs to the notorious group of Gram-negative ESKAPE pathogens. MPAO1 is also the parental strain for the widely used transposon (Tn) mutant library from the University of Washington. The complete MPAO1 genome sequence turned out to harbor several deletions and insertions compared to the PAO1-UW reference genome including numerous MPAO1-unique genes. As a second step in the model system, a biofilm flow cell based on poly (dimethylsiloxane) (PDMS) was designed to reproducibly study and identify known and novel genes related to biofilm growth and antibiotic resistance (ABR) from the Tn mutant collection. With the complete genome as optimal basis, publicly available TnSeq data were reanalyzed to identify known and novel essential genes. Furthermore, shotgun proteomics data was generated uncovering 1530 (planktonic) and 1728 (biofilm) expressed proteins, respectively, resulting in the identification of 1922 (33.1%) of the 5799 annotated P. aeruginosa MPAO1 proteins. They included proteins known to be differentially expressed during biofilm formation, and proteogenomic evidence for proteins uniquely encoded by MPAO1 as well as novel proteins.

2021-09-09 | PXD017122 | Pride

Human ex vivo Lung Perfusion: A Pre-Clinical Model for Lung Disease

Project description:We report the first use of ex vivo lung perfusion (EVLP) in the genetic and physiologic modification of lungs from deceased pulmonary arterial hypertension (PAH) patients and propose this as a translational platform to both (1) derive clinically relevant mechanistic insights into pulmonary pathophysiology and (2) to test treatments on human lungs. The EVLP consist in the perfusion of the lungs out of the body during 6 hours. It is a well established protocol in where basically lungs are on a table connected to a close circuit containing a special perfusion solution that is circulated through the pulmonary vein and artery using a pump. The circuit contains also a deoxygenator. The perfusion temperature and flow are adjusted gradually and after 20 mins of perfusion the ventilation is initiated. Every hour lungs are recruited in order to assess pulmonary function and collect perfusate samples. In addition to perfusate, tissue samples from the lower lobe of the left lung and bronchial alveolar lavage (BAL) are collected at times T0, 3 and 6 hr.

2015-06-02 | GSE69416 | GEO

Transcription profiling of human duodenal mucosa from healthy volunteers perfused with 0.055 M glutamine (10 ml/min) in saline at 10 cm distally from the pylorus for 4 h or continuous injection of 0.055 M glucose in saline

Project description:Intestinal perfusion of a 40-cm segment of the small intestine in 8 healthy volunteers. 2 test days, overnight fast. Gastroduodenoscopy for tissue sampling and positioning of perfusion catheter. Continuous injection of 0.055 M glutamine (10 ml/min) in saline at 10 cm distally from the pylorus for 4 h or continuous injection of 0.055 M glucose in saline. After the injection a second gastroduodenoscopy takes place for tissue sampling. In total we have 4 samples per individual (placebo-before; placebo-after; glutamine-before; and glutamine-after injection.

2007-12-06 | E-MEXP-941 | biostudies-arrayexpress

Epididymosomes convey different repertoires of miRNAs throughout the epididymis

Project description:Epididymosomes are small membrane vesicles (50-500nm) secreted by epididymal epithelial cells and involved in post-testicular sperm maturation. While their role in protein transfer to the sperm membrane is well acknowledged, we unveil here their capacity to vehicle microRNAs (miRNAs), which are potent regulators of post-transcriptional gene expression. Using a global microarray approach, we showed that epididymosomes providing from two discrete bovine epididymal regions (caput and cauda) possess distinct miRNA signatures. In addition, we established that miRNA repertoires contained in epididymosomes differ from those of their parent epithelial cells, suggesting that miRNA populations released from the cells may be selectively sorted. Binding of DilC12-labeled epididymosomes to primary cultured epididymal cells was measured by flow cytometry and indicated that epididymosomes from the median caput and their miRNA content may be incorporated into distal caput epithelial cells. Overall, these findings reveal that distinct miRNA repertoires are released into the intraluminal fluid in a region-specific manner and could be involved in a novel mechanism of intercellular communication throughout the epididymis via epididymosomes. We determined the miRNA profiles of epididymosomes isolated by perfusion from caput and cauda regions of the epididymis and compared it with the miRNA content of epididymal epithelial cells from the same regions.

2013-07-01 | E-GEOD-44365 | biostudies-arrayexpress

Cell Data-Indenpendent acquisition LC-MS/MS

Project description:In this work, a microwell-chip was prepared and modified. The microwell-chip was used for extraction of metabolites and subsequent protein digestion. Next, direct electrospray ionization mass spectrometry (ESI-MS) was adopted for metabolome identification and a data independent acquisition (DIA)-MS approach was established for simultaneous proteome profiling and phosphoproteome analysis. In particular, application of this strategy provides a multi-omics view of cellular changes.

2021-11-08 | PXD025634 | Pride

Effect of GSK3368715 on GBM patient samples, kept in a novel perfusion device for 8-days

Project description:Glioblastoma patient samples were microdissected into ~20mg pieces and put onto a novel perfusion device, within an hour of resection. Samples were left for 8 days, at a flow rate of 3ul/min, with a media change at day 4. Treatment was with 1uM GSK3368715. Please refer to Barry et al. Lab-on-chip 2023 for details.

2023-05-09 | GSE226721 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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