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Small non-coding RNAs in early equine osteoarthritis synovial fluid

ABSTRACT: Small non-coding RNAs in early equine osteoarthritis synovial fluid

PROVIDER: PRJEB34747 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3580111_1.fastq.gz	Fastqsanger.gz
	ERR3580111_2.fastq.gz	Fastqsanger.gz
	ERR3580112_1.fastq.gz	Fastqsanger.gz
	ERR3580112_2.fastq.gz	Fastqsanger.gz
	ERR3580113_1.fastq.gz	Fastqsanger.gz

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Small non-coding RNAs in early equine osteoarthritis synovial fluid

Project description:Small RNA isolated from synovial fluid of the metacarpophalangeal joints of horses. Horses either had minimal signs of osteoarthritis based on macroscopic and microscopic joint scoring or early (mild) osteoarthritis. Differential expression of small non-coding RNAs was undertaken.

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Small non-coding RNAs in extracellular vesicles derived from equine synovial fluid and plasma in a model of equine osteoarthritis

Project description:We studied extracellular vesicles (EVs) from plasma and synovial fluid in an in vivo model of equine osteoarthritis by investigating longitudinal samples. EVs were isolated using size exclusion chromatography from plasma and synovial fluid of four horses subjected to an osteochondral fragment model of osteoarthritis at 0, 10, 35, 42, 49, 56, 63 days with relevant controls.EV RNA was extracted and subject to small RNA sequencing on an Illumina NovaSeq SP using 100bp, single end reads. After mapping against EquCab.3.0 and miRBase v22.1 differential expression analysis was undertaken with edgeRv3.28 using a quasi-likelihood negative binomial generalized log-linear model. We identified a panel of altered small non-coding RNAs.

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Investigation of MicroRNA Biomarkers in Equine Distal Interphalangeal Joint Osteoarthritis

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Project description:Osteoarthritis (OA) is the most common equine joint disease characterised by cartilage degradation and changes to other joint tissues severely effecting welfare and performance leading to early retirement. It results in substantial morbidity and mortality, but our understanding of the pathophysiological mechanisms involved is limited. There are no disease modifying therapeutics available, with OA medication offering symptomatic relief only. Early diagnosis is thus important, as substantial joint pathology is usually present at the time of clinical diagnosis. Thus, biomarkers of early-stage OA are actively sought, and among these, extracellular vesicles (EVs) are emerging as potential candidates. Here we use a SWATH MS approach to profile the protein cargo of EVs derived from equine plasma and synovial fluid.

2023-10-24 | PXD041515 | Pride

Small non-coding RNAs in extracellular vesicles derived from equine synovial fluid and plasma in a model of equine osteoarthritis

Project description:Small non-coding RNAs in extracellular vesicles derived from equine synovial fluid and plasma in a model of equine osteoarthritis

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miRNA sequencing of synovial fluid derived extracellular vesicles between normal and osteoarthritis (OA) patients

Project description:To determine whether extracellular vesicles were also present in human disease, we isolated and evaluated extracellular vesicles from synovial fluid from normal and OA patients at relatively advanced ages (70 - 80 years). Here we report the altered expression of synovial fluid extracellular vesicles-derived miRNAs in osteoarthritis compared to normal patients with age-relate degeneration to investigate potential biomarkers for OA diagnosis. The OA donors had clinical evidence of OA based on pain that led to total joint arthroplasty.

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Transcriptomic response in osteoarthritis determined by single-cell RNA sequencing in a naturally occurring equine model

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Gene expression in synovial membranes from patients with early and end-stage osteoarthritis

2011-11-01 | GSE32317 | GEO

Equine synovial fluid

Project description:The aim of the study was to characterise the protein complement of synovial fluid (SF) in health and osteoarthritis (OA) using liquid chromatography mass spectrometry (LC-MS/MS) following peptide-based depletion of high abundance proteins. SF was used from nine normal and nine OA Thoroughbred horses. Samples were analysed with LC-MS/MS using a NanoAcquity™ LC coupled to a LTQ Orbitrap Velos. In order to enrich the lower-abundance protein fractions protein equalisation was first undertaken using ProteoMiner™. Progenesis-QI™ LC-MS software was used for label-free quantification. In addition immunohistochemistry, western blotting and mRNA expression analysis was undertaken on selected joint tissues.The number of protein identifications was increased by 33% in the Proteominer™ treated SF compared to undepleted SF. A total of 754 proteins were identified in SF. A subset of 10 proteins were identified which were differentially expressed in OA SF. S100-A10, a calcium binding protein was upregulated in OA and validated with western blotting and immunohistochemistry. Several new OA specific peptide fragments (neopeptides) were identified.The protein equalisation method compressed the dynamic range of the synovial proteins identifying the most comprehensive SF proteome to date. A number of proteins were identified for the first time in SF which may be involved in the pathogenesis of OA. We identified a distinct set of proteins and neopeptides that may act as potential biomarkers to distinguish between normal and OA joints.

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Gene expression in synovial membranes from patients with early and end-stage osteoarthritis

Project description:Osteoarthritis is characterized by degeneration of cartilage and bone in the synovial joints. Recent findings suggest that inflammation may play a role in osteoarthritis, with synovitis being associated with the clinical symptoms of osteoarthritis. Furthermore, we have found that levels of inflammatory complement components are abnormally high in the synovial fluid of individuals with osteoarthritis. To determine whether synovial membranes could be a source of complement and other inflammatory molecules in osteoarthritic joints, we characterized the expression of genes in synovial membranes from patients with early-stage or end-stage osteoarthritis. Samples of synovial membrane were obtained from the suprapatellar pouch of patients with osteoarthritis who were treated at the Hospital for Special Surgery. Specifically, samples were from 10 patients with early-stage knee osteoarthritis who were undergoing arthroscopic procedures for degenerative meniscal tears (with documented cartilage degeneration but no full-thickness cartilage loss, Kellgren Lawrence score </=2), and from 9 patients with end-stage knee osteoarthritis ( diffuse full thickness cartilage erosion) who were undergoing total knee joint replacement. Raw data from microarray analysis of healthy synovial membranes, which were run on the same platform and array as our osteoarthritic samples, were downloaded from the NCBI Gene Expression Omnibus (accession number GSE12021) and used for comparison. The 19 new Samples of this Series were analyzed (RMA) together with 7 previously submitted healthy individual Samples (GSM175810, GSM175812, GSM176290, GSM176291, GSM176292, GSM176268, GSM176269). The complete RMA data are provided as a supplementary file on the Series record. The GSE12021 reanalyzed data are also provided as a supplementary file on the Series record. GSE32317_12genes.txt includes data from figure 1 of the paper.

2011-11-01 | E-GEOD-32317 | biostudies-arrayexpress

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