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RNA Sequencing facilitates quantitative analysis of differently expressed genes with negative control (NC), siHASML, and siHuR treatment in rheumatoid fibroblast-like synoviocytes

ABSTRACT: To determine the mechanism of abnormal activity of RA FLS, we have done some research and found out that lncRNA HASML and protein HuR have some effects on migration and invasion of RA FLS. To more deeply explore how HASML and HuR regulate the functions of RA FLS, RNA sequencing analysis was used to evaluate the transcriptome of siHASML and siHuR treatment and negative control (NC) group. A P-value less than 0.05 was considered significant.

ORGANISM(S): Homo sapiens

PROVIDER: GSE188208 | GEO | 2022/11/04

REPOSITORIES: GEO

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Project description:Rheumatoid arthritis (RA) fibroblast‐like synoviocytes (FLS) derived from hip and knee have distinctive DNA methylation and transcriptome patterns in interleukin (IL)‐6 signaling and Janus kinase (JAK)–signal transducers and activators of transcription (STAT) pathways. To determine the functional effects of these joint‐specific signatures, we evaluated how RA hip and knee FLS differ in their response to IL‐6.Hip or knee RA FLS were obtained after arthroplasty. Previously published datasets on epigenetic landscape of FLS were mined to identify joint‐specific IL‐6–related epigenomic differences. RNA sequencing was performed on five RA hip and five knee FLS treated with or without IL‐6. Differential gene expression was determined using edgeR software. STAT3 phosphorylation was measured using bead assays. Sensitivity to tofacitinib was evaluated by measuring CCL2 inhibition using quantitative polymerase chain reaction. Assay for Transposase‐Accessible Chromatin sequencing and histone chromatin immunoprecipitation sequencing datasets from RA FLS were analyzed to identify epigenomic differences between hip and knee. Differential chromatin accessibility was associated with IL‐6, IL‐6R, and JAK1 genes. H3K27ac was also differentially marked at other JAK‐STAT–related genes, including STAT3‐STAT5A region. Principal component analysis of RNA sequencing data confirmed segregation between RA hip and knee FLS under basal conditions, that persisted following IL‐6 treatment. STAT3 phosphorylation after IL‐6 was significantly higher in knee than hip FLS and was highly correlated with JAK1 protein levels. Knee FLS were less sensitive to the JAK inhibitor tofacitinib than hip FLS. RA hip and knee FLS have distinct transcriptomes, epigenetic marks, and STAT3 activation patterns in the IL‐6 pathway. These joint‐specific differences might contribute to a differential clinical response in individual joints to targeted therapies such as JAK inhibitors.

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RNA Sequencing facilitates quantitative analysis of differently expressed genes with negative control (NC), siHASML, and siHuR treatment in rheumatoid fibroblast-like synoviocytes

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