Differential gene expression of RAW 264.7 macrophages in response to the RGD peptide lunasin with and without lipopolysaccharide stimulation

Lunasin is a novel peptide from soybean with demonstrated chemopreventive property. We compared the effect of lunasin on gene expression of RAW 264.7 macrophages with and without lipopolysaccharide (LPS)-stimulation. Our hypothesis was that lunasin will have a differential effect in RAW 264.7 gene expression in a normal and challenged state. Analysis of the microarray data using False Discovery Rate (FDR) method resulted in the identification of 340 up-regulated and 162 down-regulated genes (FDR p-value <0.05) associated with simultaneous treatment of lunasin and LPS for 24 h. Treatment of lunasin with no LPS for 24 h resulted in the up-regulation of 855 genes and down-regulation of 397 genes. Pre-treatment of lunasin for 24 h resulted in the up-regulation of 35 genes and down-regulation of 65 genes in LPS-stimulated RAW 264.7 macrophages. GeneVenn analysis of these three sets of genes showed that there are 66 genes common among the three groups which are mostly associated with regulation of cell death, ion binding and transcription as datamined by DAVID. Analysis of the 838 genes unique to lunasin alone by functional annotation clustering tool showed that lunasin mostly affected genes associated with RNA processing, apoptosis and protein kinase activity. Further datamining of these genes by ingenuity pathway analysis (IPA) showed that lunasin affected genes involved in cellular growth and proliferation, cellular function and maintenance, and cell to cell signaling and interaction. These findings support the potential chemopreventive and chemotherapeutic use of lunasin against cancer.