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Tumor angiogenesis and its regulation by p53-induced degradation of hypoxia-inducible factors 1 alpha are discussed. It has been shown that homozygous deletion of the p53 tumor suppressor gene using homologous recombination in a human cancer cell line promotes neovascularization and growth of tumor xenografts in nude mice. That p53 promotes Mdm2-mediated ubiquitination and proteasomal degradation of the HIF-1 alpha subunit of hypoxia inducible factor 1 (HIF-1). HIF-1 is a heterodimeric transcription factor that regulates cellular energy metabolism and angiogenesis responding to insufficient oxygen. Amplification of normal HIF-1-dependent responses to hypoxia via loss of p53 function contributes to the angiogenic switch during tumorigenesis.

Byline: Vinhthuy Phan, Allen Thomas, Kriangsiri Malasri, Carrie Hayes Sutter We propose a novel method to estimate editing efficiency by adenosine deaminases that act on RNA (ADARs). The method employs the notion of stability of secondary structure in the vicinity of edited sites during transcription. Such an analysis of 'dynamic' structural motifs of RNA is important because as a pre-spliced RNA is being transcribed and elongated, its entire structure, and thus its local structures, may change drastically. Our simulation showed that the stability of structures in the vicinity of edited sites correlates moderately highly with editing efficiency of edited sites recently established in laboratory experiments.

Hypoxia-inducible factor 1 (HIF-1) is a transcription factor that mediates cellular and systemic homeostatic responses to reduced [O.sub.2] availability in mammals, including angiogenesis, erythropoiesis, and glycolysis. HIF-1 activity is controlled by the [O.sub.2]-regulated expression of the HIF-1[Alpha] subunit. Under nonhypoxic conditions, HIF-1[Alpha] protein is subject to ubiquitination and proteasomal degradation. Here we report that missense mutations and/or deletions involving several different regions of HIF-1[Alpha] result in constitutive expression and transcriptional activity in nonhypoxic cells. We demonstrate that hypoxia results in decreased ubiquitination of HIF-1[Alpha] and that missense mutations increase HIF-1[Alpha] expression under nonhypoxic conditions by blocking ubiquitination.

Abstract: The yeast Saccharomyces cerevisiae transcription factor Yap1 mediates an adaptive response to oxidative stress by regulating protective genes. H2O2 activates Yap1 through the Gpx3-mediated formation of a Yap1 Cys303–Cys598 intramolecular disulfide bond. Thiol-reactive electrophiles can activate Yap1 directly by adduction to cysteine residues in the C-terminal domain containing Cys598, Cys620, and Cys629. H2O2 and N-ethylmaleimide (NEM) showed no cross-protection against each other, whereas another thiol-reactive chemical, acrolein, elicited Yap1-dependent cross-protection against NEM, but not H2O2. Either Cys620 or Cys629 was sufficient for activation of Yap1 by NEM or acrolein; Cys598 was dispensable for this activation mechanism. To determine whether Yap1 activated by H2O2 or thiol-reactive chemicals elicits distinct adaptive gene responses, microarray analysis was performed on the wild-type strain or its isogenic single-deletion strain Δyap1 treated with control buffer, H2O2, NEM, or acrolein. Sixty-five unique H2O2 and 327 NEM and acrolein Yap1-dependent responsive genes were identified. Functional analysis using single-gene-deletion yeast strains demonstrated that protection was conferred by CTA1 and CTT1 in the H2O2-responsive subset and YDR042C in the NEM- and acrolein-responsive subset. These findings demonstrate that the distinct mechanisms of Yap1 activation by H2O2 or thiol-reactive chemicals result in selective expression of protective genes. [ABSTRACT FROM AUTHOR]

Microarray technology has greatly aided the identification of genes that are expressed differentially. Statistical analysis of such data by multiple comparisons procedures has been slow to develop, in part, because methods to cluster the results of such comparisons in biologically meaningful ways have not been available. We isolated and analyzed, by Northern blot and GeneChip, replicate liver RNA samples (n = 4/group) from rats fed with control diet or diet containing one of three chemopreventive compounds, selected because their pharmacological activities, including RNA expression response, are relatively well understood. We report on a classification tree, based on the results of nonparametric multiple comparisons, which results in the bipolar hierarchical clustering of genes in relation to their response to treatment. In addition to identifying treatment-responsive genes, application of this procedure to our test study identified the known pharmacological relationships among the treatment groups without supervision. Also, small treatment-specific subsets of genes were identified that may be indicative of additional pharmacophores present in the test compounds.