Meniscal degradation is considered a driver of osteoarthritis (OA) progression, but the underlying mechanisms leading to age-related meniscus degeneration remain unknown. This study aimed to identify key genes and pathways involved in meniscal degradation through a computational analysis. Gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database. Differential expression gene (DEG) analysis was performed using DESeq2 accompanied by functional enrichment analysis, protein–protein interaction (PPI) and clustering analysis. Additionally, gene set enrichment analysis (GSEA) was performed. A total of 85 mRNAs (DEMs) and 8 long non-coding RNAs (DE LncRNAs) were found to be differentially expressed in OA meniscus tissues. Among 85 DEMs, 12 genes were found to be known OA-related genes, whereas 15 genes acted as transcription regulators, including RUNX2 and TBX4, which were identified as effector genes for OA. Enrichment analysis revealed the implication of DEMs in cartilage-degradation-related processes, including inflammatory pathways, lipid metabolism, extracellular matrix organization and superoxide/nitric oxide metabolic processes. Target genes of DE lncRNAs were found to be involved in chondrocyte differentiation and pathways related to cartilage degradation. A comparative analysis of meniscus, synovium and cartilage datasets identified three genes (GJB2, PAQR5 and CLEC12A) as being differentially expressed across all three OA-affected tissues, which were implicated in inflammatory and cholesterol metabolism processes. Our results support that shared mechanisms lead to meniscal and cartilage degradation during OA progression, providing further insights into the processes underlying OA pathogenesis and potential therapeutic targets for knee OA.

Background/Objectives: Emerging evidence shows long non-coding RNAs (lncRNAs) as critical regulators of osteoarthritis (OA) progression, often acting in complex networks with microRNAs (miRNAs). In our study, we investigated the potential regulatory function of the lncRNA MEG3/miR-21-5p axis in the OA phenotype of chondrocytes. Methods: Differential gene expression analysis in damaged vs. intact cartilage was performed, re-analyzing existing public RNA-seq data. MiRTarBase, LncRNADisease, and Open Targets databases were utilized to identify miR-21-5p target genes and OA-associated lncRNAs and genes. Functional enrichment analysis and protein–protein interaction (PPI) network construction were performed using the DAVID and STRING databases, respectively. MEG3, miR-21-5p, SOX5, COL2A1 and ACAN mRNA expressions were assessed by qRT-PCR. The role of the MEG3/miR-21-5p axis in OA chondrocytes was examined using transfection experiments. Results: Eighty-one lncRNAs displayed significant differences in expression between damaged and intact cartilage, including MEG3. Bioinformatic analysis indicated that MEG3 interacts with miR-21-5p, while SOX5 was identified to be a putative target of miR-21-5p. MEG3 and SOX5 expression levels were significantly downregulated in OA chondrocytes, whereas miR-21-5p expression was upregulated. Silencing of MEG3 resulted in increased miR-21-5p levels in chondrocytes. Conversely, inhibition of miR-21-5p led to increased SOX5 expression and anabolic markers COL2A1 and ACAN. Notably, MEG3 silencing significantly reduced SOX5 expression, an effect that was reversed upon miR-21-5p inhibition. Conclusions: Our findings highlight a potential regulatory role of the dysregulated MEG3/miR-21-5p axis in modulating the anabolic phenotype of chondrocytes through regulation of SOX5 expression. This novel lncRNA/miRNA/mRNA regulatory network may represent a candidate therapeutic axis for knee osteoarthritis.