SW-620 cells treated with topoisomerase I inhibitor SN-38: gene expression profiling

Abstract

Background: The goal of this study was to evaluate changes in gene expression in SW-620 cells in response to SN-38 in order to further elucidate the mechanisms by which SN-38 causes apoptosis and cell cycle arrest.

Methods: We used a quantitative gene expression microarray assay to identify the genes regulated by SN-38 treatment in colon cancer cells and confirmed our results with RT-PCR. By gene expression profiling, we first screened a proprietary list of about 22,000 genes.

Results: Treatment with SN-38 cells resulted in two-fold or greater alteration in the level of expression of 192 genes compared to control treatment. Most of the affected genes were not known to be responsive to SN-38 prior to this study. SN-38 treatment of these cells was found to affect the expression of various genes involved in DNA replication, transcription, signal transduction, growth factors, cell cycle regulation, and apoptosis, as well as other genes with unknown function. Changes in expression of 14 genes were confirmed by quantitative real-time polymerase chain reaction (RT-PCR).

Conclusion: This study leads to an increased understanding of the biochemical pathways involved in SN-38-induced apoptosis and possibly to the identification of new therapeutic targets.

Figure 1

The two independent microarray experiments behaved similarly: Genes demonstrated in this gene tree contain 840 genes that changed with a p value < 0.006 in either experiment, indicating whether the genes in the two experiments were upregulated or downregulated in the same direction in both experiments. GeneSpring software (version 6.1) was used for this gene tree (Silicon Genetics, Redwood City, CA). Values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample. Each measurement for each gene in the specific samples was divided by the median of that gene's measurements in the corresponding control samples. (A full description of these genes and detail of analysis is available on the GEO repository web site, attachment to Acc. #GSM24425-28). Mock and Pcon are the control sample for experiment 1 and experiment 2, respectively. SN-38 and PSN are the treatment sample for experiment 1 and 2, respectively.