Human rheumatoid arthritis synovial fibroblast.sbml
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ABSTRACT:
SUBMITTER: Sahar Aghakhani
PROVIDER: 286632 | Cell Collective |
REPOSITORIES: Cell Collective
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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.
2016-06-13 | PXD000740 | Pride
Project description:Macrophages from RA synovial fluids were compared to primary human blood-derived macrophages. Keywords: disease state analysis
2008-02-14 | GSE10500 | GEO
Project description:Macrophages from RA synovial fluids were compared to primary human blood-derived macrophages. Experiment Overall Design: Macrophages from synovial fluids of five RA patients were isolated by ficoll density gradient centrifugation, followed by positive selection of CD14+ cells using magnetic beads. The patientsâ?? diagnoses were determined by their physicians, in each case a Board-certified rheumatologist at the Hospital for Special Surgery, and were definite RA according to American College of Rheumatology criteria. De-identified samples were processed in an anonymous manner using a protocol approved by the Institutional Review Board of the Hospital for Special Surgery. Experiment Overall Design: Human peripheral blood mononuclear cells were isolated from venous blood of independent healthy donors by centrifugation on a Ficoll density gradient. Monocytes were obtained from PBMCs using anti-CD14 magnetic beads, and were >96% pure as verified by flow cytometry. Monocytes were differentiated into macrophages by culturing in RPMI 1640 medium supplemented with 10% fetal bovine serum and M-CSF (20 ng/ml). The viability and purity of macrophages was comparable in all conditions Experiment Overall Design: Gene expression was analyzed using Affymetrix microarrays and protocols.
2008-04-07 | E-GEOD-10500 | biostudies-arrayexpress
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.
2014-04-22 | E-GEOD-48780 | biostudies-arrayexpress
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.
2014-04-22 | GSE48780 | GEO
Project description:Synovial biopsies were obtained from rheumatoid arthritis (RA) synovium and from subjects without a joint disease to find gene upregulated during RA. The promoters of genes upregulated during RA compared to HC can be used to obtain disease-regulated gene therapy.
2016-01-27 | GSE77298 | GEO
Project description:Spots were selected that had an expression level higher than 1.6 the local background. The use of a common reference sample allows the comparison of the relative expression levels across the tissue samples. All genes were expressed relative to their median expression level across the arrays of the same microarray platform, allowing us to combine the data from the 2 platforms. Data from Lymphochip and Stanford Human cDNA arrays was combined per patient. Only genes with reliable datapoints in at least 80% of the samples were used. Subsequently, genes with the same unigene identifier were averaged in SMD. For all further analysis genes were selected that showed at least a two-fold difference in expression level in at least one array. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Using regression correlation
2007-09-13 | E-GEOD-9027 | biostudies-arrayexpress
Project description:This study performed an in-depth investigation into the myeloid cellular landscape in the synovium of Rheumatoid Arthritis (RA) patients, ‘individuals-at-risk’ of RA and healthy controls (HC). Flow-cytometric analysis demonstrated for the first time, the presence of a CD40-expressing CD206+CD163+ macrophage population dominating the inflamed RA synovium, associated with disease-activity and treatment response. RNAseq/metabolic analysis demonstrated that this macrophage population is transcriptionally distinct, displaying unique inflammatory, and tissue-resident gene signatures, has a stable bioenergetic profile, and regulates stromal cell responses. scRNAseq profiling of 67908 RA and HC synovial-tissue cells identified nine transcriptionally distinct macrophage-clusters. IL- 1B+CCL20+ and SPP1+MT2A+ are the principal macrophage clusters in RA synovium, displaying heightened CD40 gene expression, capable of shaping stromal cell responses, and importantly are enriched pre-disease onset. Combined these findings identify the presence of an early pathogenic myeloid signature that shapes the RA joint microenvironment and represents a unique opportunity for early diagnosis and therapeutic intervention.
2024-09-25 | GSE246416 | GEO
Project description:BackgroundRheumatoid arthritis (RA) is a chronic autoinflammatory disorder that affects small joints. Despite intense efforts, there are currently no definitive markers for early diagnosis of RA and for monitoring the progression of this disease, though some of the markers like anti CCP antibodies and anti vimentin antibodies are promising. We sought to catalogue the proteins present in the synovial fluid of patients with RA. It was done with the aim of identifying newer biomarkers, if any, that might prove promising in future.MethodsTo enrich the low abundance proteins, we undertook two approaches-multiple affinity removal system (MARS14) to deplete some of the most abundant proteins and lectin affinity chromatography for enrichment of glycoproteins. The peptides were analyzed by LC-MS/MS on a high resolution Fourier transform mass spectrometer.ResultsThis effort was the first total profiling of the synovial fluid proteome in RA that led to identification of 956 proteins. From the list, we identified a number of functionally significant proteins including vascular cell adhesion molecule-1, S100 proteins, AXL receptor protein tyrosine kinase, macrophage colony stimulating factor (M-CSF), programmed cell death ligand 2 (PDCD1LG2), TNF receptor 2, (TNFRSF1B) and many novel proteins including hyaluronan-binding protein 2, semaphorin 4A (SEMA4D) and osteoclast stimulating factor 1. Overall, our findings illustrate the complex and dynamic nature of RA in which multiple pathways seems to be participating actively.ConclusionsThe use of high resolution mass spectrometry thus, enabled identification of proteins which might be critical to the progression of RA.
| S-EPMC4893419 | biostudies-literature
Project description:Spots were selected that had an expression level higher than 1.6 the local background. The use of a common reference sample allows the comparison of the relative expression levels across the tissue samples. All genes were expressed relative to their median expression level across the arrays of the same microarray platform, allowing us to combine the data from the 2 platforms. Data from Lymphochip and Stanford Human cDNA arrays was combined per patient. Only genes with reliable datapoints in at least 80% of the samples were used. Subsequently, genes with the same unigene identifier were averaged in SMD. For all further analysis genes were selected that showed at least a two-fold difference in expression level in at least one array. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Keywords: disease_state_design
2007-09-13 | GSE9027 | GEO