Objectives To identify a gene expression signature in osteoarthritis (OA) synovium and genomic pathways likely to be involved in the pathogenesis of osteoarthritis.

Methods Four publicly accessible microarray studies from synovium of OA patients were integrated and a transcriptomic and network-based meta-analysis was performed. Based on pathways according to the Kyoto Encyclopaedia of Genes and Genomes (KEGG), functional enrichment analysis was performed. Meta-analysis results of OA synovium were compared to two previously published studies of OA cartilage to determine the relative number of common and specific DEGs of the cartilage and synovium.

Results According to our meta-analysis, a total of 1,350 genes were found to be differentially expressed in the synovium of OA patients as compared to that of healthy controls. Pathway analysis found 46 significant pathways in the total DEGs, and 23 and 16 pathways in the upregulated and downregulated DEGs respectively. Cell adhesion molecules (CAMs) and cytokine-cytokine receptor interaction were the most significant pathway in the upregulated and downregulated DEGs respectively. Interestingly, IL-1bβ and IL-6 were found to be downregulated in the OA synovium compared to in the healthy synovium. Comparison of meta-analysis results of OA synovium with results of two previous studies of OA cartilage identified 85 common genes and 1632 cartilage specific and 1265 synovium specific DEGs in the first study; and 142 common genes, and 856 cartilage specific and 1208 synovium specific DEGs in the second study.

Conclusion Our results show a small overlap between the DEGs of the synovium compared to DEGs of the cartilage, suggesting different pathogenic mechanisms that are specific to the synovium.