These changes occur rapidly after NGF withdrawal but become much more apparent from 12 16 hours. Other key apoptotic events such as cytochrome c release from the mitochondria and the activation of caspase 3 were also measured. Cytochrome c is released from the mitochondria following NGF withdrawal and eventually decreases in level. Simi larly, caspase 3 becomes activated and is clearly detected in sympathetic neurons deprived of NGF from 8 hours. We also detected an increase in c Jun phosphorylation Inhibitors,Modulators,Libraries at serine 63 following NGF withdrawal. This site is phosphorylated by JNKs, which are activated after NGF deprivation. Importantly, the level of c Jun phosphoryla tion increases before and peaks at 16 hours.
Therefore at 16 hours, the timepoint chosen for our Exon microarray analysis, the MLK JNK c Jun pathway has been activated in many neurons, and some Inhibitors,Modulators,Libraries cells in the population are already undergoing apoptosis. Gene expression profiling in sympathetic neurons after NGF withdrawal To identify new genes that may play a role in NGF withdrawal induced apoptosis, we performed a gene microarray analysis using Affymetrix Exon arrays and RNA isolated from sympathetic neurons that had been cultured for 16 hours in the presence of NGF, absence of NGF or absence of NGF but with the MLK inhibitor CEP 11004 added to the medium. MLKs are upstream activators of the JNK pathway in sympathetic neurons and CEP 11004 therefore blocks the increase in JNK activity and c Jun phosphorylation and protects against NGF with drawal induced death. Three independent experiments were performed.
Quality control and data analysis revealed good normalisation and reproducibility. An FDR corrected p value of 0. 05 was used as an initial cut off to identify statistically significant differences in gene expression between each of Drug_discovery the three different treatment groups. Each indivi dual comparison generated a list of differentially expressed genes which were either up or down regu lated in sympathetic neurons. When comparing the NGF and NGF treatment groups this analysis revealed 415 genes that were up regulated and 813 genes that were down regulated. A more stringent statis tical threshold with an FDR adjusted p value of 0. 01 reduced this number to 164 and 379 up and down regulated genes Inhibitors,Modulators,Libraries respectively. Further analysis revealed that of the up regulated genes with a FDR adjusted p value of 0.
01, 48 genes had a fold change of greater than 2. Similarly, the expression of 86 of the genes that were down regulated changed in level by greater than 2 fold. We also checked our microarray data for the genes previously shown to be regulated by NGF withdrawal in sympathetic neurons, such as c jun, dp5, bim, egln3 and cyclinD1 and found that their expression had changed as Inhibitors,Modulators,Libraries predicted. Importantly, the induction after NGF withdrawal of those genes pre viously defined as targets of the MLK JNK c Jun path way, c jun, bim, dp5, mkp1 was reduced by CEP 11004.