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Homo sapiens

ABSTRACT: Pain-driven transcriptome changes in synovium of knee osteoarthritis patients

PROVIDER: PRJNA389258 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5644470.fastq.gz	Fastqsanger.gz
	SRR5644480.fastq.gz	Fastqsanger.gz
	SRR5644471.fastq.gz	Fastqsanger.gz
	SRR5644481.fastq.gz	Fastqsanger.gz
	SRR5644472.fastq.gz	Fastqsanger.gz

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Pain-driven transcriptome changes in synovium of knee osteoarthritis patients

Project description:Objectives : Joint pain causes a significant morbidity in osteoarthritis (OA). The synovium as an innervated joint structure might contribute to the peripheral pain in OA. Methods : We used a hypothesis-free next generation RNA sequencing to study protein coding and small non-coding transcriptomes in knee synovial tissues of OA patients (n=10) with high and low knee pain (evaluated by visual analogue scale) followed by Gene Ontology (GO) and pathway analyses and integration of mRNAs and small RNAs data sets. Results : We showed that 33 protein-coding genes and 35 small RNAs were differentially expressed in the knee synovium of patients with high compared to low intensity knee pain, with 30 mRNAs and 14 small RNAs being upregulated and 2 mRNAs and 21 small RNAs being downregulated. Top enriched genes, such as SDIM1 and CPE encode neuronal proteins that share molecular properties with neurotrophic factor BDNF and promote neuronal survival under cellular stress, and OTOF participates in calcium-dependent synaptic exocytosis and modulation of GABAergic activity. TrkB was enriched in several gene networks, suggesting its key role in pain-related transcriptional changes in OA joint. Downregulation of PTX3 in high pain group supports an argument that inflammation and pain are independent processes in symptomatic knee OA. MiR-146a-3p and miR150 appeared as the microRNA candidates in the pathogenesis of OA-related knee pain. Conclusions : Here we uncovered the molecular complexity of pain-related transcriptome changes in the synovium of knee joints in osteoarthritis. We identified new molecular candidates in OA pain setting a firm ground for future mechanistic studies and drug discovery in OA.

2018-11-05 | GSE99662 | GEO

Spatial profiling of synovial tissue from patients with late-stage knee osteoarthritis.

Project description:Marked changes in synovial tissue are seen in knee osteoarthritis and are related to pain; however, the regulation of these processes are not fully understood. Spatial profiling was used to characterize cellular profiles and biological processes within important microenvironments in the synovium (intimal lining, sub-lining, and vessels) between patients that experience more pain compared to those that experience less pain.

2025-04-21 | GSE248454 | GEO

Dysregulated gene expression in human osteoarthritic (OA) and rheumatoid arthritis (RA) synovium

Project description:Osteoarthritis (OA) causes pain and functional disability for over 500 million people worldwide and is characterized by progressive loss of cartilage and synovial hyperplasia from the articulating surfaces of diarthrodial joints. Although the etiology of the disease is unknown, it is widely accepted that these degenerative changes arise from an imbalance of synthetic and degradative pathways that control cartilage and synovium extracellular matrix metabolism. Genome-wide U133A Affymetrix oligonucleotide array set was used to comprehensively investigate the expression pattern in non-osteoarthritis (normal) and synovium obtained from OA and rheumatoid arthritis (RA) patients undergoing knee replacement surgery. This study was undertaken to understand the disease's molecular basis better and provide relevant insight into phenotypical alterations and mechanisms involved in OA pathogenesis.

2022-08-01 | GSE206848 | GEO

E-GEOD-55235

Project description:Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation

2025-01-24 | E-GEOD-55235 | ExpressionAtlas

Gene expression profile at single cell level of synovial cells from patients with late-stage knee osteoarthritis

Project description:Innate immune cell are increased in the synovium in knee osteoarthritis. We used single cell RNA sequencing to analyze synovial cellular profiles, function, and biological processes.

2025-04-21 | GSE248453 | GEO

The novel-cell free bioactive formulation (BIOF2) modulates specific osteoarthritis’ detrimental and protective genes: A microarray analysis

Project description:A novel-cell free bioactive formulation (BIOF2), US Patent No. 9669074B2, for arthrosic chondrocytes has been recently developed and proved as effective for treating severe knee osteoarthritis, we evaluated transcriptome changes in BIOF2-treated synovial fluid cells, isolated from patients with severe knee osteoarthritis to establish BIOF2 mechanism of action.

2021-01-27 | GSE165567 | GEO

Synovial fluid proteomics from serial aspiration of ACL injured knees identifies candidate biomarkers for osteoarthritis

Project description:Patients with anterior cruciate ligament (ACL) tears have a significantly increased risk for developing knee osteoarthritis. These injuries often result in a knee effusion in response to the injury. Early changes in these effusions could be informative regarding initial steps in the development of post traumatic osteoarthritis. The purpose of this study was to test the hypothesis that the proteomics of knee synovial fluid changes over time following ACL injury.

2022-06-23 | MSV000089716 | MassIVE

Responding to ACL Injury and its Treatments: Comparative Gene Expression between Articular Cartilage and Synovium

Project description:The current study compared the transcriptomes of knee joint articular cartilage and synovium in a large animal model one year following posttraumatic osteoarthritis induction and multiple surgical treatment modalities.

2023-04-17 | GSE228848 | GEO

Single-cell sequencing of murine articular cartilage

Project description:Osteoarthritis (OA) is a degenerative joint disease characterized by progressive cartilage loss, bone remodeling, synovial inflammation, and significant joint pain, often resulting in disability. Injury to the synovial joint such as the anterior cruciate ligament (ACL) tear is the major cause of OA in young adults. Currently, there are no approved therapies available to prevent joint degeneration or rebuild articular cartilage destroyed by OA, primarily because our understanding of the cellular and molecular changes that contribute to joint damage is very limited. The synovial joint is a complex structure composed of several tissues including articular cartilage, subchondral bone, synovium, synovial fluid, and tensile tissues including tendons and ligaments. In the present study, using single-cell RNA sequencing (scRNA-seq), we examined the cellular heterogeneity in articular cartilage from mouse knee joints and determined the knee joint injury-induced early molecular changes in the chondrocytes that could contribute to OA.

2021-06-19 | GSE172500 | GEO

Identification of synovial fibroblasts subsets associated with pain and progression of knee osteoarthritis

Project description:Background: Synovial inflammation is associated with pain severity in patients with knee osteoarthritis (OA). The aim here was to determine in a population with knee OA, whether synovial tissue from areas associated with pain exhibited different synovial fibroblast transcriptomes, compared to synovial tissue from sites not associated with pain. A further aim was to compare differences between early and end-stage disease synovial fibroblasts. Methods: Patients with early knee OA (n=29) and end-stage knee OA (n=22) were recruited. Patient reported pain was recorded by questionnaire and using an anatomical knee pain map. Proton density fat suppressed MRI axial and sagittal sequences were analysed and scored for synovitis. Synovial tissue was obtained from the medial and lateral parapatellar and suprapatellar sites. RNA sequencing was performed using Illumina’s NextSeq 500 and analysed with Galaxy web platform, usegalaxy.org, and Qlucore software. Transcriptomes were functionally characterised using Ingenuity Pathway Analysis. Findings: Parapatellar synovitis was significantly associated with increased OA pain perception. Functional pathway analysis revealed that early OA painful sites mediate immune cell recruitment and promote the formation and development of neurites. Conclusion: OA disease progression and the presence of pain in early OA is associated with different synovial pathotypes. Further interrogation of these pathotypes will increase our understanding of the role of synovitis in OA joint pain and provide a rationale for the therapeutic targeting to alleviate pain in patients.

2021-10-20 | GSE176223 | GEO

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