Polyamine analogs are known to inhibit
tumorigenesis at least in part by mimicking some of the regulatory roles of natural
polyamines. To begin the identification of those signaling pathways that are involved in differential cellular responses to the synthetic conformationally restricted
polyamine analog
CGC-11093, we conducted gene expression profiling, proteomic, and genome-wide DNA methylation and
histone acetylation analyses of the HCT116
colon adenocarcinoma cell line
after treatment with this analog. Gene expression analysis was performed using Affymetrix GeneChip human genome U133 Plus 2.0 arrays. Changes in
protein expression were evaluated using 2D
polyacrylamide gels followed by LCMS/MS. DNA methylation was measured using 6,800
element CpG island microarrays. Treatment of cells with
CGC-11093 at concentrations ranging from 0.1 to 10 microM caused inhibition of cell growth and metabolic activity, but only minimally affected cell viability. Gene expression analysis showed concentration-dependent effects of
CGC-11093 on the
DNA/
RNA binding
transcription factor, cell cycle, signaling, transport, cytoskeletal/structural, and
serine protease genes. Functional gene analysis revealed distinct expression patterns related to inhibition of cell cycle control,
TGF beta signaling,
proteasome and
RNA polymerase pathways, upregulation of the aminoacyl-
tRNA synthesis pathway, and perturbations in the MAPK and Wnt signaling pathways. Microarray results were validated for selected genes with real time RT PCR. Proteomics analysis showed correlative changes in the expression of
proteins involved in the regulation of
proteasome function (
proteasome subunit Y) and
tRNA synthesis.
CGC-11093 treatment did not produce any detectable changes in DNA methylation or
histone acetylation in cells. This study validates specific target pathways for a specific conformationally restricted
polyamine analog and suggests the utility of combined gene and DNA methylation microarrays along with proteomic analyses as a useful approach to the evaluation of the mechanisms of action of anticancer drugs.