An orchestrated gene expression component of neuronal programmed cell death revealed by cDNA array analysis

Abstract

Programmed cell death (PCD) during neuronal development and disease has been shown to require de novo RNA synthesis. However, the time course and regulation of target genes is poorly understood. By using a brain-biased array of over 7,500 cDNAs, we profiled this gene expression component of PCD in cerebellar granule neurons challenged separately by potassium withdrawal, combined potassium and serum withdrawal, and kainic acid administration. We found that hundreds of genes were significantly regulated in discreet waves including known genes whose protein products are involved in PCD. A restricted set of genes was regulated by all models, providing evidence that signals inducing PCD can regulate large assemblages of genes (of which a restricted subset may be shared in multiple pathways).

Figure 1

Temporal expression clusters of genes regulated by potassium and serum-withdrawal. (Left) Hierarchical clustering was used to order 234 significantly regulated genes. Each colored row represents an expression profile for an individual gene. From left to right, control (C), 1, 3, 6, 12, and 24 h post-KS-W expression values for each gene were scaled based on the number of standard deviations from the mean intensity of each gene. Scaled expression values were color-coded such that red, yellow, and blue indicate above, at, and below mean intensity, respectively. The distance between branches in the dendrogram is proportional to the relatedness between expression patterns based on a Euclidean metric; neighboring genes are most alike. (Right) For the four major branches (Late, Middle, Early, and Immediate Early) we graphed the average profile (n = total number for each class) ± the standard deviation. Supplemental data, Table 4 provides the gene expression data.

Figure 2

Genes regulated by neuronal programmed cell death. 885 regulated genes were clustered (gene expression data, supplemental data, Table 5). Two classes are shown. Treatments and time points: SA 1, 3, 6, 12, and 24 h; KS-W 1, 3, 6, 12, and 24 h; K-W C, 1, 3, 6, and 12 h; KA treatment C, 2, 4, 8, and 12 h. Category I genes were regulated by all treatments eliciting PCD (KS-W, K-W, and KA). Category II genes were regulated by actD-sensitive models (KS-W and K-W), but not by actD-insensitive KA treatment.