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RNAseq analysis of peripheral blood and synovial fluid neutrophils from rheumatoid arthritis patients

ABSTRACT: RNAseq analysis of peripheral blood and synovial fluid neutrophils from rheumatoid arthritis patients

PROVIDER: PRJNA646457 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12228143.fastq.gz	Fastqsanger.gz
	SRR12228144.fastq.gz	Fastqsanger.gz
	SRR12228145.fastq.gz	Fastqsanger.gz
	SRR12228146.fastq.gz	Fastqsanger.gz
	SRR12228147.fastq.gz	Fastqsanger.gz

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Project description:Rheumatoid arthritis (RA) is a chronic autoinflammatory disorder that affects small joints. Despite intense efforts, there isno definitive marker yet for early diagnosis RA and for monitoring the progression of this disease. We sought to catalog the proteins present in the synovial fluid of patients with rheumatoid arthritis. To identify lower abundance proteins, we undertook two approaches – we depleted the abundant proteins using a multiple affinity removal system (MARS14) column and we enriched glycoproteins using a lectin affinity column. The peptides were analyzed by LC-MS/MS on a high resolution Fourier transform mass spectrometer.

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PROTEOMIC ANALYSIS OF EXTRACELLULAR VESICLES FROM RHEUMATOID ARTHRITIS SYNOVIAL FLUID

Project description:Previously, extracellular vesicles (EVs) from rheumatoid arthritis (RA) synovial fluid (SF) have been reported to stimulate the release of pro-inflammatory mediators in recipient cells. However, mechanistic details are unclear and contaminants in EV enrichments might have compromised previous observations. We recently developed a novel, size exclusion chromatography (SEC)-based method of EV isolation capable of high-quality enrichments from human synovial fluid. Here, we employed this method in combination with high resolution mass spectrometry to accurately characterise the SF EV proteome and investigate contributions of SF EVs to inflammatory processes in RA.

2021-04-01 | PXD015145 | Pride

Expression data from Rheumatoid Arthritis synovial tissue samples

Project description:Rheumatoid arthritis (RA) is a complex and clinically heterogeneous autoimmune disease. Microarray analysis of 83 synovial samples provides insight into the expression-level differences between patients at the site of disease activity. Synovial samples from Rheumatoid Arthritis patients were obtained during joint resection and profiled using microarrays.

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Data in support of Proteomic analysis of synovial fluid from rheumatic arthritis and spondyloarthritis patients

Project description:Objective. To analyse the pathogenesis of the diseases rheumatoid arthritis (RA) and spondyloarthritis (SpA) we investigated the protein composition in synovial fluid from the patients. Methods. Fifty-six synovial fluid (SF) were analysed with non-gel based proteomics from patients with RA (32) and SpA (24). Rheumatoid factor was measured in plasma, and cell-free DNA was measured in SF. Results. Two hundred proteins were quantified in the samples. The inflammatory proteins were more abundant in the RA group, specially proteins from neutrophil granulocytes. Cell-free DNA (cfDNA) in the SF was statistically associated with proteins that are known to form neutrophil extracellular traps (NETs). Plasma C-reactive protein (CRP), was correlated to other acute phase proteins in the SF. Minimal correlation was seen between acute phase proteins and proteins in NETs. Conclusions. The results show that in the synovial cavity in vivo neutrophils form NETs. This result sustains that neutrophils from RA patients are activated and are likely to undergo NETosis resulting in SF cfDNA specific of arthritis pathology with NETosis.

2021-09-08 | PXD010723 | Pride

Proteome of neutrophils upon migration towards inflamed synovial fluid

Project description:Analysis of neutrophil proteomic alterations induced by migration towards inflamed joints in juvenile idiopathic arthritis (JIA). In this experiment neutrophil proteomes were investigated after migration towards JIA synovial fluid in an in vitro model of a synovial membrane, compared to neutrophils incubated in synovial fluid without migration. The migration model consisted of transwell inserts with human knee synoviocytes on the undersides and HMEC endothelial cells on the insides, placed in wells containing medium with 10 % JIA synovial fluid.

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