Imatinib is a selective bcr-abl tyrosine-kinase inhibitor, successfully used as standard therapy for patients with chronic myelogenous leukemia (CML) in chronic phase. We examined the effect of Imatinib on the gene expression transcriptome pattern of CD34 positive hematopoietic stem and progenitor cells of 6 patients with newly diagnosed CML following the first week of therapy. Affymetrix U133A 2.0 microarrays covering 21.722 probe sets were used to analyze and compare the gene expression profiles of CD34+ cells from peripheral blood of 6 patients with newly diagnosed CML in chronic phase before and 7 days after the initiation of Imatinib first line therapy. One patient was female and 5 male. Their median age was 61 years (range 32–79 years). In addition, quantitative molecular monitoring of bcr-abl was performed using Light Cycler technology. Using a supervised hierarchical cluster analysis of the gene expression data we found that 303 genes were differentially expressed with a lower bound of at least 1.2 fold (−2.58 to −1.2 and 1.2 to 2.09). Of these, 183 genes were down-regulated and 120 genes were up-regulated comparing day 1 with day 7. A considerable number of the down-regulated genes are involved in the regulation of cell cycle (CDC2, CDC20, CCNB1, CCNB2) and DNA replication (TOP2A, POLE2, MCM-complex). In contrast, genes coding for proteins governing adhesion and cell migration were up-regulated (CD44, L-Selectin). The observations of the gene expression data of the aforementioned genes could be confirmed by quantitative real-time PCR. After 10 months of Imatinib therapy (range 6–13 months) all 6 patients reached in median a 3 log reduction (range 1.5–3 log reduction) of their bcr-abl mRNA. Bcr-abl FISH analysis confirmed that the majority of CD34+ cells examined were Ph-Chromosome positive. These data indicate that in the early phase of treatment Imatinib mainly acts as an inhibitor of cell cycle and replication which results in a decreased proliferation. The silencing of the Ph-Chromosome positive cells is associated with an up-regulation of genes coding for adhesion during the first week of therapy.

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