Transcriptomic effects of TNFa in primary fibroblast-like synovial cell cultures

Gene expression profiles in synovial biopsies from patients with rheumatoid arthritis (RA) display a high level of plasticity related to disease activity and response to therapy. In order to identify TNFa-dependent genes in ex vivo RA or other synovial biopsies, we generated the present set of data using primary fibroblast-like synovial cell (FLS) cultures incubated overnight in the presence or the absence of TNFa. FLS were purified from knee synovial biopsies obtained in one patient with RA, and one patient with osteoarthritis. For this experiment, cells between passage 7 and 9 were cultured in the presence or the absence of 10 ng/ml human recombinant TNFa. After overnight incubation, cells were detached, total RNA was extracted, amplified and labeled using a standard Affymetrix procedure, and hybridized on HGU133 Plus2.0 slides.