Microarray profiling analysis of long non-coding RNAs expression in osteoarthritis

Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or <-2.0-fold change; p<0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, QPCR was used to validate chip results. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA. OA cartilage were collected from 19 patients undergoing total knee joint replacement due to severe OA, and normal cartilage were collected from 11 patients (trauma, thromboangiities obliterans, or osteosarcoma, or limb amputation) without history of rheumatoid arthritis or OA Expression profiling of cartilage-normal (n=5) and cartilage-OA (n=5) samples.