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ABSTRACT: metagenomics-NGS apply on Synovial tissue

PROVIDER: PRJNA613786 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11408500.fastq.gz	Fastqsanger.gz
	SRR11408501.fastq.gz	Fastqsanger.gz
	SRR11408502.fastq.gz	Fastqsanger.gz
	SRR11408503.fastq.gz	Fastqsanger.gz
	SRR11408504.fastq.gz	Fastqsanger.gz

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metagenomics NGS study

Project description:metagenomics NGS study

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The role of distinct synovial tissue macrophage populations in shaping synovial tissue microenvironment

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Identification of distinct synovial fibroblast subsets associated with pain and progression of knee osteoarthritis using single-cell RNA sequencing

Project description:Synovial inflammation is associated with pain severity in patients with knee osteoarthritis (OA). The aim here was to determine in a population with knee OA, whether synovial tissue from areas associated with pain exhibited different synovial fibroblast subsets, compared to synovial tissue from sites not associated with pain. A further aim was to compare differences between early and end-stage disease synovial fibroblast subsets. Parapatellar synovitis was significantly associated with the pattern of patient-reported pain in knee OA patients. Synovial tissue from sites of patient-reported pain exhibited a differential transcriptomic phenotype, with distinct synovial fibroblast subsets in early OA and end-stage OA. Functional pathway analysis revealed that synovial tissue and fibroblast subsets from painful sites promoted fibrosis, inflammation and the growth and activity of neurons. The secretome of fibroblasts from early OA painful sites induced neurite outgrowth in dorsal root ganglion neurons. Sites of patient-reported pain in knee OA is associated with a different synovial tissue phenotype and distinct synovial fibroblast subsets. Further interrogation of these fibroblast pathotypes will increase our understanding of the role of synovitis in OA joint pain and provide a rationale for the therapeutic targeting of fibroblast subsets to alleviate pain in patients.

2021-10-20 | GSE176308 | GEO

Extracellular vesicles derived from synovial inflammatory macrophages induce the onset of osteoarthritis in a FMRP-selectively sorted manner [RNA-seq]

Project description:Purpose:Next Generation Sequencing has revolutionized the effect of EVs secreted by synovial inflammatory macrophages on the cartilage of OA progression. The goals of this study are to compare NGS-derived cartilages transcriptome profiling (RNA-seq) between exosomes derived from synovial inflammatory macrophages and PBS treated OA rats model. The key biological processes and siginaling pathway were identified with immunofluorescence (IF), Transmission electron microscopy (TEM) and to evaluate protocols for optimal high-throughput data analysis.

2024-10-04 | GSE278832 | GEO

A MicroRNA Next-Generation-Sequencing Discovery Assay (miND) For Genome-Scale and Absolute Quantitation of Circulating MicroRNA Biomarkers

Project description:The plasma levels of tissue-specific microRNAs can be used as prognostic and diagnostic biomarkers for chronic and acute diseases. Thereby, the combination of diverse miRNAs into biomarker signatures using multivariate statistics seems especially powerful in view to tissue and condition specific miRNA shedding into the plasma. Although Next-Generation Sequencing (NGS) technology enables to analyse circulating microRNAs on a genome-scale level, it suffers from potential biases (e.g. adapter ligation bias) and lacks absolute transcript quantitation. In order to develop a robust NGS discovery assay for genome-scale quantitation of circulating microRNAs we first evaluated the sensitivity, repeatability and ligation bias of four commercially available small RNA library preparation protocols. The protocol from RealSeq Biosciences was selected based on its performance and usability, and coupled with a novel panel of exogenous small RNA spike-in controls to enable absolute quantitation and ensure comparability of data across independent NGS experiments. The established MicroRNA Next-Generation-Sequencing Discovery Assay (miND) was validated for its relative accuracy, precision, analytical measurement range and sequencing bias and was considered fit-for-purpose for microRNA biomarker discovery. Summarized, all these criteria were met and thus our analytical platform is considered fit-for-purpose for microRNA biomarker discovery from plasma, serum, cerebrospinal fluid (CSF), synovial fluid (SF), or extracellular vesicles (EV) extracted from cell culture medium in the setting of any diagnostic, prognostic or patient stratification need.

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Next Generation Sequencing to understand the pathogenic role of synovial fibroblasts in experimental models of arthritis

Project description:The goal of this study is to define the pathophysiology of synovial fibroblasts in chroninc joint inflammation using NGS-derived synovial transcriptome profiling (RNA-seq) Methods: Synovial fibroblasts were isolated by FACs sorting [CD45-CD31-Popdoplanin+] from the synovium of healthy mice and mice undergoing experimental Collagen-Induced Arthritis (12 weeks old)(CIA). Methods: Whole Transcriptome Profiling of healthy and CIA synovial fibroblasts were generated by deep sequencing, in triplicate, using Illumina NextSeq™ 500 platform. Libraries were prepared using polyA selection (TruSeq stranded mRNA kit). Methods: The sequence reads that passed quality filters were aligned to mouse reference genome (GRCM38) using Hisat2 version 2.1.0. we mapped about 30 million sequence reads per sample (75 bp, paired-end) Methods: Featurecounts version 1.4.6 was used to quantify reads counts. Data quality control, non-expressed gene filtering, median ratio normalization (MRN) implemented in DESeq2 package and identification of differentially expressed (DE) genes were done using the R bioconductor project DEbrowser. Results: Results: We detected several differentially expressed (DE) genes in CIA synovial fibroblasts compared to naïve cells. These included 298 up-regulated genes and 88 down-regulated (>2 fold, adjp <0.05). DE genes reflected the reflecting the hyperplasia and activation observed during chronic joint disease. Pathways associated to DE genes were cell cycle and cell division and inflammatory response. Conclusions: our study shows pathophysiological changes associated to inflammatory synovial fibroblasts in a model of rheumatoid arthritis. Cells were directly isolated from fresh tissue, providing a valuable tool to study stromal inflammation.

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Project description:To investigate changes in miRNA expression in the synovial tissue, miRNA microarray was performed at day 14 after ACLT and revealed that several miRNA expressions were changed more than 1.5-fold. We chose to analyze the role of miR-21 in joint pain after ACLT because it had the highest signal intensity among the increased miRNAs. Quantitative PCR confirmed that miR-21 expression in synovial tissue was significantly increased 14 days after ACLT.

2019-10-30 | GSE139532 | GEO

Loss of synovial tissue macrophage homeostasis precedes Rheumatoid Arthritis clinical onset

Project description:To investigate the transcriptional profiles of distinct macrophage subsets residing within the inflammed RA synovium. RNA sequencing was perfomed on FACS sorted CD206+CD163+ and CD206-CD163- synovial tissue macrophages from RA synovial tissue and fluid samples.

2024-09-10 | GSE246421 | GEO

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

Project description:We used single-cell RNA sequencing to characterize the heterogeneity of equine synovial fluid and synovial tissue in a healthy and osteoarthritic joints.

2024-06-21 | GSE254840 | GEO

Identification of Altered MicroRNA Expression Patterns in Synovial Sarcoma

Project description:MicroRNAs (miRNAs) are non-coding small RNAs that function as an endogenous regulator of gene expression. Their dysregulation has been implicated in the development of several cancers. However, the status of miRNA in soft tissue sarcomas has not yet been thoroughly investigated. This study examined the global miRNA expression in synovial sarcoma and compared the results to those in another translocation-associated sarcoma, the Ewing family of tumors, and in normal skeletal muscle. The 3D-Gene miRNA microarray platform (Toray, Kamakura, Japan) and unsupervised hierarchical clustering revealed a distinct expression pattern of miRNAs in synovial sarcoma from Ewing tumors and skeletal muscle. Thirty-five of the more than 700 miRNAs analyzed were differentially expressed in synovial sarcomas in comparison to other tissue types. There were 21 significantly up-regulated miRNAs, including some miRNAs, such as let-7e, miR-99b and miR-125a-3p, clustered within the same chromosomal loci. Quantitative reverse transcription-polymerase chain reaction also demonstrated that these miRNAs were over-expressed in synovial sarcomas. The down-regulation of let-7e and miR-99b by anti-miR miRNA inhibitors resulted in the suppression of the proliferation of synovial sarcoma cells, and modulated the expression of their putative targets, HMGA2 and SMARCA5, suggesting that these molecules have a potential oncogenic role. The unique miRNA expression pattern including the over-expressed miRNA clusters in synovial sarcoma warrants further investigation in order to develop a better understanding of the oncogenic mechanisms and future therapeutic strategies for synovial sarcoma.

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