Effects of NF-κB oligonucleotide "decoys" on gene expression in P7 rat hippocampus after hypoxia/ischemia

"Decoy" oligonucleotides can be used as gene-specific nuclear factor (NF-κB) inhibitors to regulate gene expression. We applied two different decoy oligonucleotides that contained the NF-κB binding consensus sequences present in the immunoglobulin G (IgG)-κB and Bcl-x promoter into 7-day-old (P7) rat lateral ventricles before hypoxia/ischemia (HI) and compared their effects on gene expression in hippocampi to saline-treated, scrambled decoy-treated, or untreated hippocampi exposed to HI. Left hippocampi were collected at 12 hr after HI. Electrophoretic mobility shift assays (EMSAs) showed that the two decoy treatments had different effects on NF-κB binding to the IgG-κB and Bcl-x promoter-specific consensus sequences, respectively. We assessed the decoys' effects on gene expression 12 hr after HI using ribonuclease protection assays (RPAs) and Affymetrix DNA microarrays. RPAs showed that both decoys significantly decreased interleukin (IL)-1α mRNA levels but had no impact on IL-1β, IL-6, and IL-10 mRNA levels. IgG-κB decoys significantly decreased tumor necrosis factor (TNF)-α and TNF-β mRNA levels compared to minimal changes after treatment with Bcl-x decoys. DNA microarray analyses showed that Bcl-x_L decoy treatment significantly decreased Bcl-x_L mRNA levels. The decreased Bcl-x_L mRNA levels after Bcl-x decoy treatment was confirmed by RPA analysis. DNA microarray data also indicated that several other genes were affected by both decoys. Our results suggest that different NF-κB decoy treatments could differentially regulate transcriptional responses to central nervous system trauma. Careful design of decoy sequences, however, is essential to acquire selective effects on cell death outcome.