Activation changes the spectrum but not the diversity of genes expressed by T cells

Abstract

During activation T cells are thought to change their patterns of gene expression dramatically. To find out whether this is true for T cells activated in animals, the patterns of genes expressed in resting T cells and T cells 8 and 48 hr after activation were examined by using Affymetrix gene arrays. Gene arrays gave accurate comparisons of gene expression in the different cell types because the expression of genes known to vary during activation changed as expected. Of the approximately 6,300 genes assessed by the arrays, about one-third were expressed to appreciable extents in any of the T cells tested. Thus, resting T cells express a surprisingly large diversity of genes. The patterns of gene expression changed considerably within 8 hr of T cell activation but returned to a disposition more like that of resting T cells within 48 hr of exposure to antigen. Not unexpectedly, the activated T cells expressed genes associated with cell division at higher levels than resting T cells. The resting T cells expressed a number of cytokine receptor genes and some genes thought to suppress cell division, suggesting that the state of resting T cells is not a passive failure to respond to extant external stimuli.

Figure 1

Comparison of gene expression in resting and activated T cells. Poly(A) RNA was prepared and converted into fluorescent-labeled cRNA as described in Materials and Methods. The levels of cRNAs derived from different genes were measured by using Affymetrix Gene Arrays and expressed as average differences. The plots compare genes that had average differences greater than 50 in the T cell type against which the comparisons were made. Genes with average differences ≤0 in the index T cell type were omitted from the analyses. These were 57 genes in A, 53 genes in B, and 78 genes in C. The lines drawn on the graphs represent differences in average difference of 2-fold between the two samples considered. (A) Comparison of average differences for gene expression in T cells 8 hr after activation and resting T cells, with 2,758 genes considered. (B) Comparison of average differences for gene expression in T cells 48 hr after activation and resting T cells, with 2,762 genes considered. (C) Comparison of average differences for gene expression in T cells 48 hr after activation and 8 hr after activation, with 2,592 genes considered.