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Integration of clinical and multi-omics data identifies changes in the composition and activity of autologous-conditioned plasma that correlate with outcomes in patients with knee osteoarthritis

ABSTRACT: Integration of clinical and multi-omics data identifies changes in the composition and activity of autologous-conditioned plasma that correlate with outcomes in patients with knee osteoarthritis

PROVIDER: PRJNA661061 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12573762.fastq.gz	Fastqsanger.gz
	SRR12573763.fastq.gz	Fastqsanger.gz
	SRR12573764.fastq.gz	Fastqsanger.gz
	SRR12573765.fastq.gz	Fastqsanger.gz
	SRR12573766.fastq.gz	Fastqsanger.gz

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Integration of clinical and multi-omics data identifies changes in the composition and activity of autologous-conditioned plasma that correlate with outcomes in patients with knee osteoarthritis

Project description:Autologous blood-derived products such as platelet-rich plasma (PRP) or autologous-conditioned plasma (ACP) have been used for managing symptoms of knee osteoarthritis (OA); however, the outcomes are highly variable due to limited information about the characteristics of these products, and how they impact clinical responses. We hypothesized that the clinical response ACP in patients with knee OA will correlate with the biologic activity and composition of the ACP administered. To test our hypothesis, we enrolled 51 patients with mild-moderate knee OA. We collected clinical information at baseline, and patient reported outcomes at 6 weeks and 6 months after ACP injection. We evaluated the composition of ACP by multiplex ELISA, and the biologic activity of the same aliquots using an in vitro biologic assay paired with gene expression analyses. Patients were stratified as responders and non-responders to ACP based on achievement of minimal clinically important differences in patient reported outcomes collected at 6 weeks and 6 months. RNA sequencing revealed that ACP modulates inflammatory responses in a co-culture of macrophages and fibroblast-like synoviocytes (fibroblasts); using this data, we selected specific genes to evaluate the biologic activity of ACP in vitro. Comparison of ACP from responders and non-responders revealed differences in the composition and activity of ACP between these groups. By integrating clinical and multi-omics data, we uncovered changes in the composition and biologic activity of ACP that may correlate with outcomes in knee OA patients.

2021-09-02 | GSE157364 | GEO

Synovial Macrophage Activation Profiles in Experimental Knee Osteoarthritis

Project description:To investigate differences in gene expression of synovial macrophages in experimental rat knee post traumatic osteoarthritis.

2024-03-22 | GSE216932 | GEO

Bulk RNA-seq of human knee osteoarthritis synovium

Project description:To classify knee osteoarthritis (OA) synoviums according to gene expression patterns, we performed RNA-seq using synovial tissues obtained from OA patients and non-OA patients.

2025-01-07 | GSE283079 | GEO

Transcriptome sequencing of synovial tissues of knee osteoarthritis rats.

Project description:Using transcriptome sequencing to screen the differntent expression genes in MIA-induced knee osteoarthritis (KOA) model rats compared with normal rats.

2024-06-22 | GSE206678 | GEO

Single cell RNA-seq of human knee osteoarthritis synovium

Project description:To classify knee osteoarthritis (OA) synoviums according to gene expression patterns, we performed single cell RNA-seq using synovial tissues obtained from OA patients.

2025-01-07 | GSE283080 | GEO

Regulatory constraint and selection during human knee evolution drive modern osteoarthritis risk

Project description:The evolution of human bipedalism exposed the knee to unique biomechanical challenges, requiring changes in knee anatomy giving rise to the modern-day configuration. In order to better understand the relationship between derived knee morphology and the genetic factors associated with osteoarthritis risk, we performed epigenetic profiling of murine forelimb/hindlimb growth plates to identify regulatory elements shaping formation of specific knee structures, identifying signals of ancient positive selection upon which more recent genetic drift overlaps risk-associated loci. Our functional analyses of an osteoarthritis-risk variant within a reproducibly-associated locus establishes a novel model for studying this degenerative disease.

2020-04-16 | GSE122877 | GEO

In vitro effects of equine autologous conditioned serum and autologous equine serum on inflamed chondrocyte pellets

Project description:The aim of the study was to investigate the effects of autologous equine serum (AES) incubated for 24 h and autologous conditioned serum (ACS) on inflamed equine chondrocyte pellets in vitro.

2023-04-19 | GSE152253 | GEO

Genetic Components of Knee Osteoarthritis (GeCKO) Study: The Osteoarthritis Initiative

Project description:Genetic Components of Knee Osteoarthritis (GeCKO) Study: The Osteoarthritis Initiative

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Osteoarthritis-related changes in gene expression in knee articular chondrocytes in a rat model of osteoarthritis.

Project description:Cartilage destruction in osteoarthritis (OA) results from disturbed chondrocyte metabolism. Here, we used microarrays to show that TGF alpha and CCL2 are simultaneously upregulated in a rat model of OA and cooperate to drive cartilage degradation. The goals of the experiments included here were to a) characterize gene expression in knee joint articular chondrocytes at various stages of development of OA (2 and 8 weeks after surgical induction of OA), and b) to establish trends in gene expression among groups of genes related to the TGF alpha-EGFR axis, over time, in OA. The model chosen to study these results has been previously validated (Appleton, CT et al, 2007, Arthritis Rheum) and used to describe similar gene expression results at a different time point (4 weeks) after induction of OA. The rat model of OA involves surgical destabilization of the knee joint, followed by forced low-intensity mobilization over several weeks; a sham surgery is used as the control (representing a healthy non-OA knee joint) wherein a surgical incision is made but not structural (i.e. ligamentous) modification is made to the joint. Altogether, our data indicate that TGF and CCL2 cooperate to drive cartilage degradation in osteoarthritis. A total of 12 samples were analyzed. 3 replicates were used per condition: OA surgery at 2 weeks, OA surgery at 8 weeks, Sham (control) surgery at 2 weeks and Sham surgery at 8 weeks. Expression of OA samples was assessed relaitve to Sham (control) expression levels.

2012-11-15 | E-GEOD-42295 | biostudies-arrayexpress

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

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