Gene expression was evaluated in clones of the acute lymphoblastic leukemic cell line CEM that were sensitive or resistant to apoptosis evoked by the glucocorticoid, dexamethasone (Dex). Founding clones CEM-C7 (glucocorticoid sensitive) and CEM-C1 (glucocorticoid resistant) were subcloned to maximize uniformity of each population studied. Among subclones of C1, our original pseudodiploid clone of glucocorticoid-resistant cells, we found a high proportion of hyperploid clones. Most C1 subclones were glucocorticoid resistant but two C1 subclones were found to be revertants to glucocorticoid sensitivity. Glucocorticoid receptor content of the C1 subclones varied almost 5-fold but higher quantity of receptors did not guarantee steroid sensitivity. Gene expression analysis was carried out on microchips containing representations for approximately 12,600 human genes. When a group of four subclones from C1 (three glucocorticoid-resistant and one glucocorticoid-sensitive revertant) were compared with the glucocorticoid-sensitive subclone CEM-C7-14 for basal gene expression, the four C1 subclones clustered closely and far from C7-14. Thus, basal gene expression in the C1 subclones differed for a large number of genes from that in the C7 subclone. Reversion to glucocorticoid sensitivity did not cause a major shift in basal gene expression to a more C7-like state. Three clones (one revertant glucocorticoid sensitive from C1 subclone, one C7 sensitive subclone, and one C1 glucocorticoid-resistant subclone) were compared for the genes regulated by treatment for 20 hours with 10(-6)M Dex. This interval brings the cells to a point just before the onset of apoptosis. We tested the hypothesis that a distinctive set of genes would be regulated in the glucocorticoid-sensitive clones. This proved to be so. In three experiments, at our chosen levels of discrimination, 39 genes were consistently induced > or = 2.5-fold and 21 genes were consistently reduced > or = 2-fold in glucocorticoid-sensitive clones but not in the glucocorticoid-resistant clone. The glucocorticoid-resistant clone showed induction or reduction of 88 genes different from those regulated in the glucocorticoid-sensitive clones. These data support our hypothesis and further show that the glucocorticoid-resistant clone is capable of responding to steroid but with a different set of genes. We propose that a general metabolic switch accounts for the alteration.