Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tensile strain and altered synovial tissue metabolism in human knee osteoarthritis

ABSTRACT: To investigate the physiologic responses of whole osteoarthritic synovium to cycle tensile strain. We obtained 3 matched synovial tissue samples from 6 patients undergoing total knee arthroplasty, subjected them to cyclic tensile strain, and then performed gene expression profiling analysis using RNA seq from each cyclic tensile strain protocol.

ORGANISM(S): Homo sapiens

PROVIDER: GSE205196 | GEO | 2022/09/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Differential expression analysis of human small RNAs in young normal, old normal (protected)) and old osteoarthritis (unprotected ) knee cartilage

Project description:Human cartilage taken from young normal knees following anterior cruciate ligament repair and osteoarthritic cartilage; old normal (protected) and old osteoarthritic (unprotected) following total knee arthroplasty. Total RNA extracted using mirVana miRNA isolation kit (Life Technologies). The Affymetrix Flash Tag labelling kit was used to prepare samples for hybridisation onto Affymetrix miRNA 4.0 arrays.

2017-12-31 | E-MTAB-5716 | biostudies-arrayexpress

Differential expression analysis of small RNAs in young normal and old osteoarthritis cartilage

Project description:Human cartilage taken from young normal knees following anterior cruciate ligament repair and osteoarthritic cartilage following total knee arthroplasty. Total RNA extracted using mirVana miRNA isolation kit (Life Technologies). The Affymetrix Flash Tag labelling kit was used to prepare samples for hybridisation onto Affymetrix miRNA 4.0 arrays.

2017-12-31 | E-MTAB-5715 | biostudies-arrayexpress

Effect of cyclic tensile stretch on meniscus cells in the presence and absence of IL-1

Project description:Meniscus injuries are highly prevalent and are linked to the development of post-traumatic osteoarthritis (PTOA). The inflammatory cytokine IL-1 is elevated in synovial fluid following knee injuries, causes degradation of meniscus tissue, and inhibits meniscus repair. Cyclic tensile stretch has been shown to modulate the expression of pro-inflammatory cytokines and degradative enzymes induced by IL-1; however, there remains a dearth of knowledge on global effects of loading on meniscus cell phenotype and transcriptomic profiles. In this study, we performed mRNA-Seq on meniscus cells isolated from inner and outer zone regions of porcine menisci subjected to cyclic tensile strain in the presence and absence of IL-1 to identify cellular responses to mechanical load, identify differences in response to load based on zonal characteristics, and identify IL-1 induced inflammatory responses modulated by load.

2021-12-23 | GSE191321 | GEO

Pain-driven transcriptome changes in synovium of knee osteoarthritis patients

Project description:Objectives : Joint pain causes a significant morbidity in osteoarthritis (OA). The synovium as an innervated joint structure might contribute to the peripheral pain in OA. Methods : We used a hypothesis-free next generation RNA sequencing to study protein coding and small non-coding transcriptomes in knee synovial tissues of OA patients (n=10) with high and low knee pain (evaluated by visual analogue scale) followed by Gene Ontology (GO) and pathway analyses and integration of mRNAs and small RNAs data sets. Results : We showed that 33 protein-coding genes and 35 small RNAs were differentially expressed in the knee synovium of patients with high compared to low intensity knee pain, with 30 mRNAs and 14 small RNAs being upregulated and 2 mRNAs and 21 small RNAs being downregulated. Top enriched genes, such as SDIM1 and CPE encode neuronal proteins that share molecular properties with neurotrophic factor BDNF and promote neuronal survival under cellular stress, and OTOF participates in calcium-dependent synaptic exocytosis and modulation of GABAergic activity. TrkB was enriched in several gene networks, suggesting its key role in pain-related transcriptional changes in OA joint. Downregulation of PTX3 in high pain group supports an argument that inflammation and pain are independent processes in symptomatic knee OA. MiR-146a-3p and miR150 appeared as the microRNA candidates in the pathogenesis of OA-related knee pain. Conclusions : Here we uncovered the molecular complexity of pain-related transcriptome changes in the synovium of knee joints in osteoarthritis. We identified new molecular candidates in OA pain setting a firm ground for future mechanistic studies and drug discovery in OA.

2018-11-05 | GSE99662 | GEO

Genome-wide analysis of mechano-responsive gene expression by tenocytes in fascicles subjected to cyclic tensile strain

Project description:Analysis of mechano-regulation of tenocyte metabolism at gene expression level. The hypothesis tested in the present study was that cyclic tensile strain influence the balance of anabolism/catabolism of tenocytes. Results provide important information of the response of tenocyte to cyclic tensile strain, such as specific mechano-responsive genes, up- or down-regulated specific anabolic/catabolic cellular functions. Keywords: gene expression array-based, stress response, functional analysis

2008-07-23 | GSE12206 | GEO

Cyclic tensile strain enhances the expression of Indian hedgehog and progression of ossification of the human cervical posterior longitudinal ligament

Project description:The initiation and/or progression of ossification of the posterior longitudinal ligament (OPLL) is associated with cyclic tensile strain, but the pathomechanism of OPLL remains unclear. Indian hedgehog (Ihh) and its related signaling are key factors in normal enchondral ossification. However, the relation of OPLL to Ihh is unclear. The purpose of this study is to investigate the contribution of mechanical strain to OPLL and the relation of Ihh to OPLL. Cultured posterior longitudinal ligament cells were subjected to 24 hours of cyclic tensile strain and then analyzed by microarray.

2016-06-22 | E-GEOD-83569 | biostudies-arrayexpress

Genome-wide DNA methylation study of hip and knee osteoarthritic and healthy cartilage reveals embryonic organ and skeletal system morphogenesis as major pathways involved in osteoarthritis

Project description:Cartilage samples were collected from hip or knee joint replacement patients either due to primary OA or hip fractures as controls. DNA was extracted from the collected cartilage and assayed by Illumina Infinium HumanMethylation450 âBeadChip array, which allows for the analysis of >480,000 CpG sites. Bisulphite converted DNA from 5 hip osteoarthritic, 6 knee osteoarthritic and 7 hip healhty cartilage samples were hybridised to the Illumina Infinium HumanMethylation450 âBeadChip array

2016-07-01 | E-GEOD-73626 | biostudies-arrayexpress

Expression data from total knee arthroplasty patients

Project description:Ischaemic preconditioning is a method of protecting tissue against ischaemia-reperfusion injury. It is an innate protective mechanism that increases a tissue's tolerance to prolonged ischaemia when it is first subjected to short burst of ischaemia and reperfusion. It is thought to provide this protection by increasing the tissue's tolerance to ischaemia, therby reducing oxidative stress, inflammation and apoptosis in the preconditioned tissue. We used microarrays to investigate the genomic response induced by ischaemic preconditioning in muscle biopsies taken from the operative leg of total knee arthroplasty patients in order to gain insight into the ischaemic preconditioning mechanism. Patients undergoing primary knee arthroplasty were randomised to control and treatment (ischaemic preconditioning) groups. Patients in the treatment group received a preconditioning stimulus immediately prior to surgery. The ischaemic preconditioning stimulus consisted of three five-minute periods of tourniquet insufflation on the lower operative limb, interrupted by five minute periods of reperfusion. All patients had a tourniquet applied to the lower limb after the administration of spinal anaesthesia, as per normal protocol for knee arthroplasty surgery. Muscle biopsies were taken from the quadriceps muscle of the operative knee at the immediate onset of surgery (T0) and at 1 hour into surgery (T1). Total RNA was extracted from biospies of four control and four treatment patients and hybridised to the Affymetrix Human U133 2.0 chip.

2010-04-12 | E-GEOD-21164 | biostudies-arrayexpress

Muscle transcriptome analysis following Total Knee Arthroplasty with Tourniquet

Project description:Transcriptome profiling was performed on muscle biopsies from patients immediately before Total Knee Arthroplasty and two hours after TKA and tourniquet application.

2016-02-01 | GSE75432 | GEO

Genome-wide Expression Profiles of Subchondral Bone in Osteoarthritis

Project description:To date, all of the prior osteoarthritic microarray studies in human tissue have focused on the overlying articular cartilage, meniscus, or synovium but not the underlying subchondral bone. In our previous study, our group developed a methodology for high quality RNA isolation from site-matched cartilage and bone from human knee joints, which allowed us to perform candidate gene expression analysis on the subchohndral bone (published on Osteoarthritis and Cartilage on Dec/5/2012 (doi: 10.1016/j.joca.2012.11.016). To the best of our knowledge, the current study is the first to successfully perform whole-genome microarray profiling analyses of human osteoarthritic subchondral bone. We believe our comprehensive microarray results can improve the understanding of the pathogenesis of osteoarthritis and could further contribute to the development of new biomarker and therapeutic strategies in osteoarthritis.

2013-10-24 | GSE51588 | GEO

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