Temporal profiling of gene expression during neurogenesis and remodeling in the olfactory epithelium at short intervals after target ablation

Neurogenesis in the olfactory epithelium (OE) is induced by olfactory bulbectomy (OBX), which effectively axotomizes olfactory sensory neurons (OSNs) and removes their synaptic targets, resulting in apoptosis. We used Affymetrix high-density oligonucleotide arrays to investigate changes in gene expression during the initiation of signaling in pathways that regulate apoptosis and neurogenesis in the murine OE at 2, 8, 16, and 48 hr after bilateral OBX compared with sham-operated controls. We focused on the regulation of a defined set of genes associated with apoptosis, stem/progenitor cell regulation, and cell cycle progression because of the activation of these processes in OE degeneration and remodeling after OBX. After data scrubbing and categorical analysis, one-way ANOVA identified 72 genes (4.9% of the "Present" known genes) as being significantly regulated (P < 0.05) at one or more time points; 50 were defined as differentially regulated, with a false discovery rate at 10%. Significant changes in gene expression occurred in all categories as early as 2 hr post-OBX, with the greatest number of differentially regulated genes at 16 and 48 hr. Hierarchical cluster analysis and correlation coefficients were used to identify similarities in patterns of gene expression changes within and across categories. Validation was performed with SuperArray macroarrays and real-time RT-PCR. Our results confirmed the participation of many genes in known signaling pathways and identified changes in the expression of 42 genes not previously identified as participating in apoptosis and neurogenesis in the OE. Additionally, our analyses indicated the early involvement of genes regulating cytoskeletal reorganization and angiogenesis in the response to OBX. These studies are an important first step in defining early time-dependent changes in gene expression following target ablation that lead to neurogenesis in the olfactory sensory epithelium.