Examination of the MAPK pathway and Bim expression in patient samples. (A) Microarray analysis of total RNA isolated from samples of circulating tumor cells from 7 patients before romidepsin infusion (0 hours), at 4 hours after initiation of the infusion (4 hours), and 24 hours after initiation of the infusion (24 hours). An annotated list of genes that were shown to be under the control of the MAPK pathway was compiled from a series of studies and selected for analysis (supplemental Table 1). Ratios for all genes versus pretreatment values were log transformed and mean centered. An additional filter was applied to the untransformed ratios such that only genes with at least 1 ratio >2 were considered. A heatmap was then generated by using the centroid method for hierarchical clustering and Pearson correlation for the similarity metric. (B) Quantitative PCR analysis of selected MAPK-regulated genes as well as MDR-1 was performed in a subset of patients with CTCL treated with romidepsin. Genes observed to be decreased in the array in (A) were confirmed in a separate set of messenger RNA samples. (C) Bim expression as detected by immunohistochemistry in skin biopsies collected before or while on study (left column) and at disease progression (right column) from 4 patients treated with romidepsin. Magnification ×40.