Effects of IL-6 on the gene expression profile of CD4+ T cells early during activation. (A) FACS-sorted CD4+ T cells were activated with anti-CD3 and anti-CD28 in the absence or presence of IL-6 for 16 h. The gene expression profile from total RNA was examined by Affymetrix GeneChip analysis. In the volcano plot, open circles represent probe sets for which expression is changed more than twofold up or down after IL-6 treatment, whereas dots represent all other probe sets. The number of genes exceeding the threshold was the largest among the 10 datasets obtained by permutation of sample labels, yielding statistical significance of differential expression at P = 0.1 (the minimum value) and a false discovery rate <19% (the minimum being 10%). The blue line encloses 99% of the probe sets under the null hypothesis, obtained by permutation of sample labels. The IL-21 gene is marked with an arrow. (B) Heat maps representing the relative expression of genes among IL-6–treated and control samples. Genes were sorted within each group based on their fold change (top, highest fold induction; bottom, highest fold down-regulation). Expression statistics for each gene were centered, scaled, and mapped to a color scale. Red represents relatively low expression, whereas green represents relatively high expression. (C) Cells were purified and activated as in A, and IL-21 expression was measured by quantitative real-time RT-PCR. The means ± SEM of three experiments are shown. (D) CD4+ T cells were activated with anti-CD3 and anti-CD28 mAbs in the absence or presence of IL-6 for the indicated periods of time. Cell-culture supernatants were analyzed for IL-21 production by ELISA. The means ± SEM of four experiments are shown.