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Analysis and ceRNA network construction of differentially expressed lncRNAs and mRNAs in human osteoarthritis cartilage

ABSTRACT: This study aimed to identify differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in damaged cartilage (DC) and un-damaged cartilage (UDC) from osteoarthritis (OA) patients. RNA sequencing was performed on cartilage samples from five OA patients undergoing total knee arthroplasty. Bioinformatics analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and competing endogenous RNA (ceRNA) network construction, was conducted.

ORGANISM(S): Homo sapiens

PROVIDER: GSE289464 | GEO | 2026/02/01

REPOSITORIES: GEO

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Long non-coding RNA HOTTIP promotes CCL3 expression and induces cartilage degradation by sponging miR-455-3p

Project description:Long non-coding RNAs (lncRNAs) play pivotal roles in diseases such as osteoarthritis (OA). However, knowledge of the biological roles of lncRNAs is limited in OA. We aimed to explore the biological function and molecular mechanism of HOTTIP in chondrogenesis and cartilage degradation. We used the human mesenchymal stem cell (MSC) model of chondrogenesis, in parallel with, tissue biopsies from normal and OA cartilage to detect HOTTIP, CCL3, and miR-455-3p expression in vitro. Biological interactions between HOTTIP and miR-455-3p were determined by RNA silencing and overexpression in vitro. We evaluated the effect of HOTTIP on chondrogenesis and degeneration, and its regulation of miR-455-3p via competing endogenous RNA (ceRNA). Our in vitro ceRNA findings were further confirmed within animal models in vivo. Mechanisms of ceRNAs were determined by bioinformatic analysis, a luciferase reporter system, RNA pull-down, and RNA immunoprecipitation (RIP) assays. We found reduced miR-455-3p expression and significantly upregulated lncRNA HOTTIP and CCL3 expression in OA cartilage tissues and chondrocytes. The expression of HOTTIP and CCL3 was increased in chondrocytes treated with interleukin-1β (IL-1β) in vitro. Knockdown of HOTTIP promoted cartilage-specific gene expression and suppressed CCL3. Conversely, HOTTIP overexpression reduced cartilage-specific genes and increased CCL3. Notably, HOTTIP negatively regulated miR-455-3p and increased CCL3 levels in human primary chondrocytes. Mechanistic investigations indicated that HOTTIP functioned as ceRNA for miR-455-3p enhanced CCL3 expression. Taken together, the ceRNA regulatory network of HOTTIP/miR-455-3p/CCL3 plays a critical role in OA pathogenesis and suggests HOTTIP is a potential target in OA therapy.

2019-08-12 | PXD014988 | Pride

Single-cell RNA sequencing of chondrocytes from osteoarthritis (OA) patients and healthy controls

Project description:Osteoarthritis (OA) is a common degenerative joint disease characterized by progressive cartilage degeneration and osteophyte formation. However, the mechanisms underlying OA progression remain poorly understood. Single-cell RNA sequencing (scRNA-seq) was performed on chondrocytes from three OA patients undergoing total knee arthroplasty and three control donors undergoing arthroscopic surgery for anterior cruciate ligament (ACL) injury to explore cellular heterogeneity and dysregulated pathways. These data provide a resource for investigating the molecular mechanisms underlying OA progression.

2026-03-18 | GSE324993 | GEO

Transcriptome comparison of cartilage from patients with and without osteoarthritis

Project description:Objective: To assess the impact of osteoarthritis (OA) on the transcripts and biological process in the articular cartilage between patients with and without OA. Design: Patients undergoing arthroscopic partial meniscectomy (APM) without any evidence for OA and patients undergoing total knee arthroplasty (TKA) due to end-stage OA were consented. Healthy-appearing cartilage was garnered from the non-weight bearing site of the medial intercondylar notch. RNA preparation was subjected to SurePrint G3 human 8X60K RNA microarrays to probe differentially expressed (DE) transcripts followed by computational exploration of underlying biological processes and pathways. Real-time PCR was performed on selected transcripts to validate microarrays data. Results: We identified 603 transcripts significantly (FDR <0.05) differentially expressed (293 elevated, 310 repressed) between APM and TKA samples (1.5 fold). Among these, CFD, CSN1S1, TSPAN11, CSF1R and CD14 were the most prominent transcripts elevated in TKA group, CHI3L2, MEG3, HILPDA, COL3A1, COL27A and FGF2 were most highly repressed in TKA samples. Few long intergenic non-coding RNAs (linRNAs), and small nuclear RNAs (snoRNAs) were also differentially expressed between the two groups. Conclusions: Numerous transcripts with potential relevance to the pathogenesis of OA are DE in OA and non-OA cartilage. These data suggest an involvement of metabolic signaling and epigenetic markers (lincRNAs, snoRNAs) in cartilage.

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RNA-Seq analysis of human intact and damaged osteoarthrtitic cartilage following total knee replacement.

Project description:This experiment captures the expression of genes between two sites of human cartilage within the same patients to allow investigation of genomic responses to damage during osteoarthritis. Eight patients with symptomatic OA undergoing total knee replacement (n=8, age range 65-79 years, mean age 70.3) were used in this study. Cartilage from paired osteochondral samples were isolated from the intact PLC (posterior lateral condyle) and the damaged DMC (distal medial condyle) for RNA-seq analysis.

2016-04-06 | E-MTAB-4304 | biostudies-arrayexpress

Characterization of the cartilage DNA methylome in knee and hip osteoarthritis.

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2015-09-02 | GSE63695 | GEO

MiR-335-5p escaped from circKIAA0586 adsorption contributes to mechanical overloading-induced cartilage degeneration by targeting HELLS (circRNA-Seq)

Project description:Mechanical overload is essential to cartilage degeneration during osteoarthritis (OA) development. Recent studies have confirmed that circular RNAs (circRNAs) are mechanically sensitive and that the circRNA-associated competitive endogenous RNA (ceRNA) network regulates cartilage degeneration and OA development. However, the involvement of the circRNA-associated ceRNA network in chondrocyte senescence induced by mechanical overloading remains unestablished.Here,we examined the circRNA, miRNA and mRNA expression of chondrocytes subjected to mechanical overloading.

2024-11-01 | GSE274761 | GEO

MiR-335-5p escaped from circKIAA0586 adsorption contributes to mechanical overloading-induced cartilage degeneration by targeting HELLS (miRNA-Seq)

2024-11-01 | GSE274760 | GEO

MiR-335-5p escaped from circKIAA0586 adsorption contributes to mechanical overloading-induced cartilage degeneration by targeting HELLS (RNA-Seq)

2024-11-01 | GSE274759 | GEO

LOXL2 deletion in post-traumatic injury dysregulates knee joint homeostasis and promotes pain sensitivity, inflammation, and osteoarthritis

Project description:Traumatic knee injuries lead to cartilage degeneration and osteoarthritis (OA). Cartilage has limited potential for self-regeneration, and any damage can lead to structural, molecular, and functional aberrations in the knee joint. Early changes in extracellular matrix (ECM) affecting cartilage are primarily asymptomatic and progress towards knee joint dysfunction, pre-OA, and finally OA. This study aimed to elucidate the mechanism of lysyl oxidase-like 2 (LOXL2) in maintaining healthy knee joint articular cartilage, its regeneration, and potential therapeutic applications. LOXL2 loss-of-function was evaluated using Acan promoter-specific inducible Loxl2 knockout, followed by immunohistochemistry, RNA-seq, transcriptional analysis, and knee joint functional and pain analysis. Our results showed that LOXL2 deletion increases the severity of destabilized medial meniscus (DMM) -induced cartilage damage. LOXL2-overexpressing mice were protected against degenerative cartilage changes in the knee joint compared with their wild-type littermates. Interestingly, Intra-articular injection of adenovirus-delivered LOXL2 protected knee joint function, alleviated cartilage degeneration, restored treadmill running capability, and reduced allodynia. Overall, LOXL2 loss initiates cartilage damage, inflammation, and pain, leading to OA. The gain of LOXL2 protects against progressive cartilage damage and relieves pain and inflammation. Thus, we identified a novel function for LOXL2 in OA-related local pain.

2026-01-21 | GSE285114 | GEO

RNA-Seq analysis of human osteoarthritic intact cartilage following total knee replacement

Project description:Large scale RNA-Seq analysis was performed to investigate the transcriptomic response to osteoarthritis in cartilage and investigate potential subgroups of patients. Data were collected from intact knee cartilage (posterior lateral condyle) from at total of 60 patients with osteoarthritis (OA) following total knee replacement and 10 control non-OA patients following amputation.

2017-12-13 | E-MTAB-6266 | biostudies-arrayexpress

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