Gene expression profile of RA FLSs with or without ALKBH5 knockdown
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE203267 | GEO | 2023/12/31
REPOSITORIES: GEO
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Project description:To investigate how ALKBH5 modulates RA FLSs functions, we conducted m6A sequencing (MeRIP-seq) of RA FLSs. Consistent with previous studies, in both scramble controls and ALKBH5 knockdown cells, m6A modifications were highly enriched within the GGAC motif. m6A peaks are located mainly in the protein-coding region (CDS) and 3’ untranslated region (3’ UTR) of mRNA transcripts
2023-12-31 | GSE203269 | GEO
Project description:Gene expression profile of RA FLSs with or without ALKBH5 knockdown
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Project description:Platelet microparticles (PMPs) are closely related to the activity of rheumatoid arthritis, and promote the migration and invasion of rheumatoid arthritis fibroblast-like synoviocytes (RA-FLSs). In order to identify the possible mechanisms of the promotion effect on migration and invasion of RA-FLS by PMP, we used microarray analysis to detect the gene expressions of RA-FLSs after treatment with PMPs.
2017-06-06 | GSE99681 | GEO
Project description:Rheumatoid arthritis (RA) is a common chronic inflammatory joint disease characterized by persistent synovial hyperplasia and progressive destruction of joint cartilage and bone.Fibroblast-like synoviocytes (FLSs), a prominent component of hyperplastic synovial pannus tissue, are the primary effector cells in RA synovial hyperplasia and invasion. However, the underlying molecular mechanisms remain unclear. Here, we apply transcriptome to assay the regulatory networks which contribute to the proliferation, migration and invasion of RA-FLSs .
2020-01-08 | GSE128813 | GEO
Project description:Genome-wide maps of m6a state in RA FLSs with or without ALKBH5 knockdown.
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Project description:Invasive pannus, mainly composed of fibroblast-like synoviocytes (FLSs), is a hallmark of rheumatoid arthritis (RA) pathology. Secreted proteins from RA-FLS play key roles in RA invasive pannus. However, RA-FLS-derived secretome associated with invasive pannus has not been systematically investigated. Here, we first identified 843 secreted proteins from RA-FLSs treated with TNFα and IL-1β using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Functional enrichment analysis revealed that 58.5% (493 proteins) of the secretome were associated with pannus-driven RA pathologies. Among them, parallel reaction monitoring (PRM) analysis then identified 16 secreted proteins that were increased in RA SFs (117 samples) than in OA SFs (45 samples). Of them, MYH9 further showed significant positive correlations with RA pathological parameters, such as synovial hyperplasia, increased articular vascularity, and inflammation severity. Molecular and cellular experiments confirmed that MYH9 was expressed in RA-FLSs and more highly under disease-aggravating conditions, and MYH9 depletion significantly defected migration and invasion of RA-FLS in RA pannus. Our study provides a comprehensive resource of RA-FLS-derived secretome, and our results suggest MYH9 that was increased in RA SF and strongly correlated with disease severity as a potential therapeutic target for invasive pannus.
2023-06-30 | PXD041077 | Pride
Project description:The transcriptome analysis of regulatory networks in RA-FLSs
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Project description:Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammatory in joints. Macrophages are abundant in synovial tissue and fluid of RA. Macrophages extracellular traps (METs) are induced from macrophages and may generate a stable autoantigen-DNA complexes, leading to the generation of autoantibodies and development of autoimmunity. We aimed to investigate the role of METs on the biologic behaviors of FLSs from patients with RA. RA-FLS from 3 independent RA patients were treated with METs, and performed whole transcriptome sequencing on MET-treated and untreated groups in a total of 6 groups. Further, we performed bioinformatic analysis on the sequencing results (Novogene, China). The transcriptome was first explored for differentially expressed genes and the main results were visualized with a heatmap. Next, GO and KEGG enrichment analysis were performed on the differential genes. The results were visualized using dot plots to explore which functions of RA-FLS may be affected by MET and the potential pathways that affect RA-FLS function
2022-10-25 | GSE216181 | GEO
Project description:N6-methyladenosine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Here we report ALKBH5 as a new mammalian demethylase that oxidatively removes the m6A modification in mRNA in vitro and inside cells. This demethylation activity of ALKBH5 significantly affects mRNA export and RNA metabolism as well as the assembly of mRNA processing factors in nuclear speckles. Alkbh5-deficient male mice are characterized by impaired fertility resulting from apoptosis that affects meiotic metaphase-stage spermatocytes. In accordance with this defect, we have identified in mouse testes 1552 differentially expressed genes which cover broad functional categories and include spermatogenesis-related mRNAs involved in the p53 functional interaction network. We show that Alkbh5-deficiency impacts the expression levels of some of these mRNAs, supporting the observed phenotype. The discovery of this new RNA demethylase strongly suggests that the reversible m6A modification plays fundamental and broad functions in mammalian cells. RNA-seq in two cell types
2013-02-15 | E-GEOD-40132 | biostudies-arrayexpress
Project description:Inflammation-mediated oncogenesis has been implicated in a variety of cancer types. Rheumatoid synovial tissues can be viewed as a tumor-like mass, consisting of hyperplastic fibroblast-like synoviocytes (FLSs). FLSs of rheumatoid arthritis (RA) patients have pro-migratory and invasive characteristics, which may be caused by chronic exposure to genotoxic stimuli, including hypoxia and growth factors. We tested whether a transformed phenotype of RA-FLSs is associated with placental growth factor (PlGF), a representative angiogenic growth factor induced by hypoxia. Here, we identified PlGF-1 and PlGF-2 as the major PlGF isoforms in RA-FLSs. Global gene expression profiling revealed that cell proliferation, apoptosis, angiogenesis, and cell migration were mainly represented by differentially expressed genes in RA-FLSs transfected with siRNA for PlGF. Indeed, PlGF-deficient RA-FLSs showed a decrease in cell proliferation, migration, and invasion, but an increase in apoptotic death in vitro. PlGF gene overexpression resulted in the opposite effects. Moreover, exogeneous PlGF-1 and PlGF-2 increased survival, migration, and invasiveness of RA-FLSs by binding their receptors, Flt-1 and NP-1, up-regulating the expression of anti-apoptotic molecules, pErk and Bcl2. Knock-down of PlGF transcripts reduced RA-FLS proliferation in a xeno-transplantation model. Collectively, in addition to their role for neovascularization, PlGF-1 and -2 promote proliferation, survival, migration, and invasion of RA-FLSs in an autocrine and paracrine manner. These results demonstrated how primary cells of mesenchymal origin acquired an aggressive and transformed phenotype. PlGF and its receptors thus offer new targets for anti-FLS therapy. The FLSs were prepared from the synovial tissues of RA patients and incubated in DMEM supplemented with 10% FBS. Cells were cultured in RPMI supplemented with 10% FBS. There are 4 FLS samples treated with PlGF siRNA, and 4 FLS samples treated with control siRNA.
2015-01-14 | E-GEOD-64922 | biostudies-arrayexpress