Identification of genomic targets downstream of p38 mitogen-activated protein kinase pathway mediating tumor necrosis factor-α signaling

Inhibition of p38 MAPK suppresses the expression of proinflammatory cytokines such as TNF-alpha and IL- 1 beta in macrophages and fibroblast-like synoviocytes (FLS). However, there have been no genomewide studies on the gene targets of p38 MAPK signaling in synoviocytes. Microarray technology was applied to generate a comprehensive analysis of all genes regulated by the p38 MAPK signaling pathway in FLS. Gene expression levels were measured with Agilent oligonucleotide microarrays. Four independent sets of mRNA modulated by TNF-alpha and vehicle were used to measure the change of gene expression due to TNF-alpha, and three experiments were done to ascertain the effect of SB- 203580, a p38 MAPK inhibitor, on TNF-alpha- induced genes. Microarray data were validated by RT-quantitative polymerase chain reaction. One hundred fortyone significantly expressed genes were more than twofold upregulated by TNF-alpha. Thirty percent of these genes were downregulated by the p38 inhibitor SB- 203580, whereas 67% of these genes were not significantly changed. The SB- 203580- inhibited genes include proinflammatory cytokines such as interleukins and chemokines, proteases including matrix metallopeptidases, metabolism-related genes such as cyclooxygenases and phosphodiesterase, genes involved in signal transduction, and genes encoding for transcription factors, receptors, and transporters. Approximately one-third of the TNF-alpha- induced genes in FLS are regulated by the p38 MAPK signal pathway, showing that p38 MAPK a possible target for suppressing proinflammatory gene expressions in rheumatoid arthritis.