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Muscle Transcriptomic Circuits Linked to Periarticular Physiology in End-Stage Osteoarthritis.

ABSTRACT: Muscle Transcriptomic Circuits Linked to Periarticular Physiology in End-Stage Osteoarthritis.

PROVIDER: PRJNA845210 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19537851_1.fastq.gz	Fastqsanger.gz
	SRR19537851_2.fastq.gz	Fastqsanger.gz
	SRR19537852_1.fastq.gz	Fastqsanger.gz
	SRR19537852_2.fastq.gz	Fastqsanger.gz
	SRR19537853_1.fastq.gz	Fastqsanger.gz

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Muscle Transcriptomic Circuits Linked to Periarticular Physiology in End-Stage Osteoarthritis.

Project description:Long RNAseq was performed on vastus lateralis, vastus medialis, tensor fascia latae, or gluteus maximus muscle samples from patients with end-stage OA. The primary study utilized single target differential gene expression analyses coupled with network biology to determine molecular circuits in the skeletal muscle overlaying a diseased joint.

2022-12-28 | GSE205431 | GEO

Muscle transcriptomic circuits linked to periarticular physiology in end-stage osteoarthritis.

Project description:The ability of individuals with end-stage osteoarthritis (OA) to functionally recover from total joint arthroplasty is highly inconsistent. The molecular mechanisms driving this heterogeneity have yet to be elucidated. Furthermore, OA disproportionately impacts females, suggesting a need for identifying female-specific therapeutic targets. We profiled the skeletal muscle transcriptome in females with end-stage OA (n = 20) undergoing total knee or hip arthroplasty using RNA-Seq. Single-gene differential expression (DE) analyses tested for DE genes between skeletal muscle overlaying the surgical (SX) joint and muscle from the contralateral (CTRL) leg. Network analyses were performed using Pathway-Level Information ExtractoR (PLIER) to summarize genes into latent variables (LVs), i.e., gene circuits, and link them to biological pathways. LV differences in SX versus CTRL muscle and across sources of muscle tissue (vastus medialis, vastus lateralis, or tensor fascia latae) were determined with ANOVA. Linear models tested for associations between LVs and muscle phenotype on the SX side (inflammation, function, and integrity). DE analysis revealed 360 DE genes (|Log2 fold-difference| ≥ 1, FDR ≤ 0.05) between the SX and CTRL limbs, many associated with inflammation and lipid metabolism. PLIER analyses revealed circuits associated with protein degradation and fibro-adipogenic cell gene expression. Muscle inflammation and function were linked to an LV associated with endothelial cell gene expression highlighting a potential regulatory role of endothelial cells within skeletal muscle. These findings may provide insight into potential therapeutic targets to improve OA rehabilitation before and/or following total joint replacement.

| S-EPMC9762959 | biostudies-literature

Gene expression in synovial membranes from patients with early and end-stage osteoarthritis

2011-11-01 | GSE32317 | GEO

Gene expression in synovial membranes from patients with early and end-stage osteoarthritis

Project description:Osteoarthritis is characterized by degeneration of cartilage and bone in the synovial joints. Recent findings suggest that inflammation may play a role in osteoarthritis, with synovitis being associated with the clinical symptoms of osteoarthritis. Furthermore, we have found that levels of inflammatory complement components are abnormally high in the synovial fluid of individuals with osteoarthritis. To determine whether synovial membranes could be a source of complement and other inflammatory molecules in osteoarthritic joints, we characterized the expression of genes in synovial membranes from patients with early-stage or end-stage osteoarthritis. Samples of synovial membrane were obtained from the suprapatellar pouch of patients with osteoarthritis who were treated at the Hospital for Special Surgery. Specifically, samples were from 10 patients with early-stage knee osteoarthritis who were undergoing arthroscopic procedures for degenerative meniscal tears (with documented cartilage degeneration but no full-thickness cartilage loss, Kellgren Lawrence score </=2), and from 9 patients with end-stage knee osteoarthritis ( diffuse full thickness cartilage erosion) who were undergoing total knee joint replacement. Raw data from microarray analysis of healthy synovial membranes, which were run on the same platform and array as our osteoarthritic samples, were downloaded from the NCBI Gene Expression Omnibus (accession number GSE12021) and used for comparison. The 19 new Samples of this Series were analyzed (RMA) together with 7 previously submitted healthy individual Samples (GSM175810, GSM175812, GSM176290, GSM176291, GSM176292, GSM176268, GSM176269). The complete RMA data are provided as a supplementary file on the Series record. The GSE12021 reanalyzed data are also provided as a supplementary file on the Series record. GSE32317_12genes.txt includes data from figure 1 of the paper.

2011-11-01 | E-GEOD-32317 | biostudies-arrayexpress

Synovial biopsies of osteoarthritis patients

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Cartilage microRNA dysregulation during the onset and progression of mouse osteoarthritis is independent of aggrecanolysis and overlaps with candidates from end-stage human disease [miRNA]

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2025-08-05 | GSE283762 | GEO

MicroRNA-sequencing of plasma from patients in the Osteoarthritis Initiative Cohort

Project description:Objective: we aimed to identify circulating microRNAs associated with fast-progressing knee osteoarthritis (OA) as compared to slow-progressing knee OA and non-progressing knee OA using sujects from the Osteoarthritis Initiative (OAI) cohort. MicroRNA libraries were prepared from plasma using the QIAseq miRNA Library Kit (QIAGEN) and sequenced on the Illumina NextSeq550 using a single-end 75-base read protocol to an average depth of 11.6 ± 2.6 SD million reads per sample.

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MicroRNA expression profile in macrophages from rheumatoid arthritis and osteoarthritis patients

Project description:In osteoarthritis (OA) and rheumatoid arthritis (RA), many pathological alterations result from aberrant macrophage hyperactivation in the inflamed synovial membrane, and inhibition of macrophage effector functions is a therapeutic strategy in both diseases. Little is known, about the specific genetic circuits that are differentially deregulated in RA and OA macrophages. microRNA (miR) are short single stranded non-coding RNAs involved in the post-transcriptional regulation of gene expression. Altered expression of miRs has been described under various pathological conditions, including rheumatic and other autoimmune diseases. Here we compared the miR expression profile in macrophages isolated from OA and RA patients miR expression in OA and RA macrophages was analyzed using Exiqon miRCURY microarrays. Three biological replicates (patients) were analyzed. Two samples (RA vs OA) were hybridized per microarray.

2016-02-05 | E-GEOD-63745 | biostudies-arrayexpress

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