Microarray analysis of in vivo dexamethasone-induced gene expression. ALL-50 and ALL-54 engrafted mice were treated with dexamethasone 15 mg/kg or vehicle control, and cells harvested after 8 hours. GEPs of spleen-harvested cells were evaluated using microarray. The data for each condition are presented with samples from 3 randomized ALL-engrafted mice. (A) Principal component analysis of global GEPs of the ALL-50 and ALL-54 samples before (circles) and after (squares) treatment with dexamethasone. (B) Heatmap of differentially expressed genes between ALL-50 and ALL-54 after dexamethasone treatment. A list of 457 genes was generated and ranked using Limma with a formula of (x54.Dex-x54.Con)/2-(x50.Dex-x50.Con)/2 (false discovery rate [FDR] <0.05). (C) Nine genes related to either GR signaling or epigenetic modulation were selected from the Limma gene list. Relative gene expressions of the 9 selected genes and BIM (BCL2L11) in ALL-50 and ALL-54 during dexamethasone treatment were presented in a heatmap. (D) Heatmap of the dexamethasone-induced fold changes of 10 genes in a panel of 10 xenografts including 5 dexamethasone-resistant xenografts (ALL-28/-50/-55/-56/-57) and 5 dexamethasone-sensitive xenografts (ALL-26/-51/-52/-53/-54). Hierarchical clustering of the 10 genes was performed based on their fold changes on dexamethasone treatment. (E-F) Scatter plots of dexamethasone-induced fold changes of KLF13 and MYB expression in the 2 groups of dexamethasone-resistant and -sensitive xenografts. *P < .05 (Mann-Whitney U test). (G) Correlation curve of dexamethasone-induced fold changes of MYB and BCL2 expression levels in the 10 xenografts. (H) Correlation curve of dexamethasone-induced fold changes of BCL2 and BIM expression levels in the 10 xenografts. Con, vehicle control; Dex, dexamethasone.