Use of a differential subtraction method to identify genes that characterize the phenotype of cultured rheumatoid arthritis synoviocytes

OBJECTIVE: To identify the genes that characterize the distinctive phenotype of cultured rheumatoid arthritis (RA) fibroblastoid synoviocytes. METHODS: A representational difference method was used to subtract complementary DNA (cDNA) from cultured RA fibroblastoid synoviocytes with cDNA from noninflammatory osteoarthritis synoviocytes. The genes were identified by DNA sequencing, and their relative expression was determined by Northern blot analysis. RESULTS: Twenty-four genes were identified, including novel genes such as a human homolog of mouse semaphorin E and one homologous to N-acetylglucosamine-6-sulfatase. Eleven of these genes were constitutively overexpressed in the rheumatoid synoviocyte line, including a chemokine, stromal cell-derived factor 1, and several genes capable of mediating synoviocyte-leukocyte interactions, including vascular cell adhesion molecule 1 and Mac-2 binding protein. Three genes (lumican, biglycan, and insulin-like growth factor binding protein 5) encoded extracellular matrix components, suggesting that distinct stromal-synoviocyte interactions may be mediated by this phenotype. Two interferon-inducible genes of unknown function were also found, emphasizing the presence of activation-like features in the phenotype. CONCLUSION: A general method for the identification of differences in patterns of gene expression revealed that cultured RA fibroblastoid synoviocytes overexpress certain proinflammatory genes that are potentially relevant to lymphocyte and monocyte entry and interactions. The features of the genes identified in these mesenchymal cells suggest that they facilitate localization of immune reactions to the joint through leukocyte chemokinesis, cell-cell adhesion, and matrix specialization. The further characterization of these genes should help in resolving whether this phenotype is the consequence of modulation and imprinting by an inflammatory milieu or, more likely, whether it reflects the intrinsic lineage characteristics of intimal lining synoviocytes.