Analyzing gene expression profile in K562 cells exposed to sodium valproate using microarray combined with the connectivity map database

Abstract

To explore the mechanism underlying antileukaemia effect of sodium valproate, the growth and survival of the K562 cell line were investigated. Global profiles of gene expression in K562 cells exposed to sodium valproate were assessed and validated. The differentially expressed genes identified were further used to query the connectivity map database to retrieve a ranked list of compounds that act on the same intracellular targets as sodium valproate. A significant increase in cell apoptosis and a change in gene expression profile were observed in valproate-exposed K562 cells. The significant enrichment analysis of gene ontology terms for the differentially expressed genes showed that these genes were involved in many important biological processes. Eight differentially expressed genes involved in apoptosis were verified by quantitative real-time PCR. The connectivity map analysis showed gene expression profile in K562 cells exposed to sodium valproate was most similar to that of HDACi and PI3K inhibitors, suggesting that sodium valproate might exert antileukaemic action by inhibiting HDAC as well as inhibiting PI3K pathway. In conclusion, our data might provide clues to elucidate the molecular and therapeutic potential of VPA in leukaemia treatment, and the connectivity map is a useful tool for exploring the molecular mechanism of drug action.

Figure 1

Alterations in the expression levels identified by microarray were confirmed using qRT-PCR. Fold changes between K562 cell line treated with and without valproate detected by microarray were compared with those measured by qRT-PCR. In qRT-PCR assay, RNA was isolated from K562 cell line treated with or without valproate exclusively for validation of differentially expressed genes. mRNA levels were normalized with GADPH and fold changes were calculated by dividing mRNA level of each K563 cell line treated with valproate by mean mRNA level from control samples in triplicate. Data are mean values ± standard deviations of the means from three independent experiments performed in triplicate.