Profiling of H3K27ac landscape in immune cells from rheumatoid arthritis patients and healthy controls
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PROVIDER: EGAS00001005085 | EGA |
REPOSITORIES: EGA
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Project description:Comparative gene expression profiling of mononuclear cells from synovial fluid samples of rheumatoid arthritis (RA) and spondyloarthropathy (SpA) cases was performed. A total of 72 transcripts were found to be differentially expressed in RA compared to SpA, with p-value threshold of 0.05 and using the Benjamini-Hochberg False Discovery rate multiple comparison corrections. From the list, 57 transcripts were found to be upregulated in RA as compared to SpA and 15 downregulated by a fold change cut-off of 1.5-fold.
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Project description:We collected peripheral blood mononuclear cells (PBMC) from 6 RA patients and 4 healthy controls, as well as synovial fluid (SF) from the same RA patients. We then sorted B cells, CD4+ and CD8+ T cells, regulatory T cells and monocytes using flow cytometry and profiled regions marked with H3K27ac using CUT&Tag.
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Project description:Rheumatoid arthritis (RA) and spondyloarthropathy (SpA) are chronic inflammatory disorders primarily targeting joints. Although the type of inflammatory cells present in affected joints implicated in the disease pathogenesis is the same, the diseases differ in terms of disease activity and manifestation. So to comprehend the two diseases in better terms, we carried out a comparative gene expression profiling using the inflammatory mononuclear cells from knee aspirated synovial fluid samples as this joint fluid bathes the affected region thereby giving us a closer view of the pathological site. We identified 1469 differentially regulated genes. Out of 1469 differentially regulated genes, 1366 genes were upregulated in SpA and 103 genes were downregulated in SpA versus RA. The proposed study carried out mRNA expression profiling of mononuclear cells from synovial fluid samples of seven RA and five SpA cases. We have used 4X44K and 1X44K arrays from Agilent Technologies platform. Based on the RNA integrity, selected molecules were processed further using single-color microarray based gene expression. The raw data files obtained from this study were eventually analyzed with R package of the BioConductor suite.
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Project description:Rheumatoid synoviocytes, which consist of fibroblast-like synoviocytes (FLS) and synovial macrophages (SM), are crucial for the progression of rheumatoid arthritis (RA). Particularly, FLS of RA patients (RA-FLS) exhibit invasive characteristics reminiscent of cancer cells, destroying cartilage and bone, although it remains unresolved how RA-FLS exhibit invasive phenotype. RA-FLS and SM originate differently from mesenchymal and myeloid cells, respectively, but share many pathologic functions. However, the molecular signatures and biological networks representing the distinct and shared features of the two cell types are unknown. Presently, we performed global transcriptome profiling of FLS and SM obtained from RA and osteoarthritis patients. By comparing the transcriptomes, we identified distinct molecular signatures and cellular processes defining invasiveness of RA-FLS and pro-inflammatory properties of RA synovial macrophages (RA-SM), respectively. Interestingly, under interleukin1β-stimulated condition, RA-FLS newly acquired pro-inflammatory signature mimicking RA-SM without losing invasive properties. We next reconstructed a network model that delineates the shared, RA-FLS-dominant (invasive), and RA-SM-dominant (inflammatory) processes. From the network model, we selected 13 genes, including POSTN and TWIST1, as novel regulator candidates responsible for FLS invasiveness. Of note, POSTN and TWIST1 expressions were elevated in independent RA-FLS and were further instigated by interleukin1β. In vitro functional assays demonstrated the requirement of POSTN and TWIST1 for migration and invasion of RA-FLS stimulated with interleukin1β. Taken together, our systems approach to rheumatoid synovitis provides a basis for identifying novel regulators responsible for pathological features of RA-FLS and RA-SM, demonstrating how a certain type of cells acquires functional redundancy under chronic inflammatory conditions. To identify molecular signatures of FLS and MLS in RA joints, we isolated FLS from synovial tissues of RA and osteoarthritis (OA) patients, obtained synovial macrophages from synovial fluid of RA patients, and differentiated control macrophages from peripheral blood of healthy subjects. Also, we stimulated FLS with IL1β, and then analyzed gene expression profiles of both IL1β-stimulated RA-FLS and OA-FLS
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