Project description:Objective: The objective of this study was to characterize extracellular vesicles (EVs) in plasma and synovial fluid obtained from horses with and without naturally occurring post-traumatic osteoarthritis (PTOA). Animals (Samples): EVs were isolated from plasma and synovial fluid from horses with (n = 6) and without (n = 6) PTOA. Methods: Plasma and synovial fluid EVs were characterized with respect to quantity, size, and surface markers. Small RNA sequencing was performed and differentially expressed miRNAs underwent bioinformatic analysis to identify putative targets and to explore potential associations with specific biological processes. Results: Plasma and synovial fluid samples from horses with PTOA had a significantly higher proportion of exosomes and a lower proportion of microvesicles compared to horses without PTOA. Small RNA sequencing revealed several differentially expressed miRNAs including miR-144, miR-219-3p, and miR-199a-3p in plasma and miR-199a-3p, miR-214, and miR-9094 in synovial fluid EVs. Bioinformatics analysis of the differentially expressed miRNAs highlighted their potential role in fibrosis, differentiation of chondrocytes, apoptosis, and inflammation pathways in PTOA. Clinical Relevance: We have identified dynamic molecular changes in small non-coding signatures of plasma and synovial fluid EVs in horses with naturally occurring PTOA. These findings could serve to identify promising biomarkers in the pathogenesis of PTOA, to facilitate the development of targeted therapies, and to aid in establishing appropriate translational models of PTOA.
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.
Project description:This dataset contains small RNA sequencing data and mRNA capture sequencing data from 20 different human biofluids (amniotic fluid, aqueous humor, ascites, bile, bronchial lavage fluid, breast milk, cerebrospinal fluid, colostrum, gastric fluid, pancreatic cyst fluid, plasma, saliva, seminal fluid, serum, sputum, stool, synovial fluid, sweat, tear fluid and urine). In total, 180 samples were sequenced. Files are provided in fastQ format. Samples were sequenced on a NextSeq 500.
Project description:This study shows the pronounced expansion of CD8 T cell clones at sites of active inflammation within the joints of psoriatic arthritis (PsA) patients compared to blood, and characterises the gene expression of expanded clones using droplet based single cell RNA sequencing. Mononuclear cells were separated from freshly acquired paired peripheral blood and synovial fluid samples from 3 PsA patients using density gradient separation, then enriched for CD4 and CD8 T cells using FACS. Additionally, CD45+ leukocytes were enriched by FACS from the cryopreserved synovial tissue of 2 further PsA patients. All cells were then processed using a 10x Chromium Controller and sequenced by Illumina HiSeq 4000 (peripheral blood / synovial fluid) or NovaSeq with S2 flowcell (synovial tissue).
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.
Project description:To investigate the effects of soluble factors produced by synovial CD8 T cells, we stimulated human rheumatoid arthritis (RA) synovial fibroblasts with supernatants from synovial fluid CD8 T cells, blood CD8 T cells, or synovial fluid CD4 T cells stimulated with anti-CD3/CD28 antibody-coated beads. For comparison, we stimulated RA synovial fibroblasts with recombinant TNF or interferon-gamma or T cell supernatants pre-incubated with TNF-blocking antibodies.
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.
Project description:With H3K27ac chromatin immunoprecipitation we identified a disease-specific, inflammation-associated, (super-)enhancer signature in JIA patient synovial fluid-derived CD4+ memory/effector T cells. This signature consists of unique pathogenesis-associated epigenetic changes which extend beyond general T cell activation-induced alterations, indicating that disease-specific (super-)enhancers contribute to JIA pathogenesis. In addition, our analysis shows that there is a profound enrichment of JIA-related SNPs in (super-)enhancers in JIA patients compared to controls, illustrating the importance of these non-coding regions for disease pathogenesis. H3K27ac ChIP-sequencing of CD4+ memory/effector T cells derived from peripheral blood (PB) from healthy controls (HC) and PB or synovial fluid (SF) from JIA patients.
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
