Recently clusterin (CLU) was reported to be an inhibitor of NF-B pathway and involved in rheumatoid arthritis (RA) synovitis. This study was designed to decipher the molecular network linked to CLU expression in FLS (fibroblast-like synoviocytes) and evaluate the consequences of its low expression in conditions of TNF-␣ stimulation. FLS were transfected with siRNA for CLU or not and cultured for 24 and 48 h with TNF-␣ or not. Pan-genomic gene expression was assayed by DNA microarray. The gene network around CLU and gene interactions were analyzed with the Ingenuity Pathway Analysis software. Downregulation of CLU resulted in modification of the expression of genes known to be directly linked to CLU and for almost 5% of the tested genes (857 out of 17,225); the upregulation of a small group of gene (e.g., TIAM1) emphasizes the hypothetical role of CLU in the pseudotumoral characteristic of FLS. The comparison of gene expression with or without TNF stimulation allowed the classification of sampled with good concordance. Moreover, differential comparison showed that CLU downregulation in RA led to a profound modification of the TNF-␣ response as three sets of genes emerged: 497 genes modulated by siCLU transfection with TNF stimulation, 356 genes modified because of TNF stimulation only, and 484 genes modulated during TNF stimulation with CLU expression (e.g., IL-8 and Wnt signaling genes). Using a global two-way ANOVA we could identify a set of genes defining a molecular signature of TNF response directly influenced by CLU. These results (based on differential gene expression patterns) argue that CLU downregulation in FLS alters their aggressiveness in RA synovitis. rheumatoid arthritis; fibroblast-like synoviocytes; microarray; siRNA; tumor necrosis factor RHEUMATOID ARTHRITIS (RA) is a chronic inflammatory disease that has an effect on the synovial membrane, cartilage, and bone. Despite comprehensive progress in the last decade, the pathophysiological mechanisms of RA are still poorly understood (11). During RA, the synovial cells from the lining and sublining layers become activated and hyperproliferative (8). Among the identified genes modulated in RA synovitis, the clusterin (CLU) gene appears to be a potential gene of interest because it has multiple functions related to apoptosis, inflammation, proliferation, and differentiation (4, 5, 7). The different functions of CLU depend on its final maturation and localization, cytosolic or nuclear, and involve NF-B signaling and juxtanuclear aggregates (3,6,14). The predominant form of CLU is a secreted heterodimeric protein of 80 kDa (sCLU) produced from the full-length RNA. sCLU is derived from a pre-sCLU protein of 60 kDa targeted to the endoplasmic reticulum and that is glycosylated. A nuclear form of CLU has recently been described and is the resulting product of an alternative splicing (10). Overall, it appeared recently that many previously reported functions are related to the intracellular forms of the protein, especially NF-B signaling and apoptosis. Indee...