We have used microarray gene expression profiling and machine learning to predict the presence of BRAF mutations in a panel of 61 melanoma cell lines. The BRAF gene was found to be mutated in 42 samples (69%) and intragenic mutations of the NRAS gene were detected in seven samples (11%). No cell line carried mutations of both genes. Using support vector machines, we have built a classifier that differentiates between melanoma cell lines based on BRAF mutation status. As few as 83 genes are able to discriminate between BRAF mutant and BRAF wild-type samples with clear separation observed using hierarchical clustering. Multidimensional scaling was used to visualize the relationship between a BRAF mutation signature and that of a generalized mitogen-activated protein kinase (MAPK) activation (either BRAF or NRAS mutation) in the context of the discriminating gene list. We observed that samples carrying NRAS mutations lie somewhere between those with or without BRAF mutations. These observations suggest that there are gene-specific mutation signals in addition to a common MAPK activation that result from the pleiotropic effects of either BRAF or NRAS on other signaling pathways, leading to measurably different transcriptional changes.

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Cdc25 regulates entry into mitosis by regulating the activation of cyclin B/cdc2. In humans, at least two cdc25 isoforms have roles in controlling the G 2 /M transition. Here we show, using bacterially expressed recombinant proteins, that two cdc25B splice variants, cdc25B2 and cdc25B3, are capable of activating cyclin A/cdk2 and cyclin B/cdc2, but that mitotic hyperphosphorylation of these proteins increases their activity toward only cyclin B1/cdc2. Cdc25C has only very low activity in its unphosphorylated form, and following hyperphosphorylation it will efficiently catalyze the activation of only cyclin B/cdc2. This was reflected by the in vivo activity of the immunoprecipitated cdc25B and cdc25C from interphase and mitotic HeLa cells. The increased activity of the hyperphosphorylated cdc25s toward cyclin B1/cdc2 was in large part due to increased binding of this substrate. The substrate specificity, activities, and timing of the hyperphosphorylation of cdc25B and cdc25C during G 2 and M suggest that these two mitotic cdc25 isoforms are activated by different kinases and perform different functions during progression through G 2 into mitosis.Regulation of the activity of cyclin-dependent kinases (cdks) 1 underlies cell cycle progression. Cdks are regulated by a combination of factors, including cyclin association, and phosphorylations and dephosphorylations of the cdk subunit. The final step in the activation of cyclin/cdks is catalyzed by a member of the cdc25 family of dual specificity phosphatases, which remove inhibitory phosphates from Thr 14 and Tyr 15 of cdk2 and cdc2.The role and regulation of cdc25 phosphatase has been well defined in yeast and Xenopus egg systems, using a combination of genetics and biochemistry. In Schizosaccharomyces pombe, cdc25 is controlled at the transcriptional, translational, and post-translational levels. The mRNA and protein levels oscillate through the cell cycle, being maximal in G 2 , but the protein requires further post-translational modification in the form of phosphorylation for maximal activity (1, 2). Xenopus cdc25 levels do not change, but its activity is also controlled by phosphorylation and dephosphorylation (3, 4). In humans, three isoforms of cdc25 exist, cdc25A, -B, and -C. Cdc25A has a role in regulating the G 1 /S cell cycle phase transition whereas cdc25B and cdc25C regulated the G 2 /M transition (5-9). The level of mRNA for each isoform changes through the cell cycle, but the protein levels of only cdc25A and cdc25B have been reported to change in a cell cycle-dependent manner (5, 7, 9). All three cdc25s are phosphorylated in vivo, and phosphorylation has been demonstrated to regulate the activity of cdc25A and cdc25C (6, 10, 11).Whereas the in vivo substrates identified for the cdc25s to date are the Tyr-phosphorylated cyclin/cdks, cdc25 activity has usually been measured in vitro using a range of substrates, most of which are non-physiological e.g. p-nitrophenyl phosphate. The cdc25 phosphatases utilize this substrate very poorly (12), and there is e...

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