H Ressom | PubMed Health

PubMed2006

Effect of Akt inhibition on scatter factor-regulated gene expression in DU-145 human prostate cancer cells.

The cytokine scatter factor (SF) (hepatocyte growth factor) transduces various biologic actions, including cell motility, invasion, angiogenesis and apoptosis inhibition. The latter is relevant to understanding the role of SF in promoting tumor cell survival in different contexts, for example, detachment from basement membrane, growth in metastatic sites and responses to chemo- and radiotherapy. Previously, we showed that SF protects cells against apoptosis owing to DNA damage, by a mechanism involving phosphoinositol-3-kinase/c-Akt signaling. Here, we used DNA microarray assays to identify c-Akt-regulated genes that might contribute to cell protection. DU-145 human prostate cancer cells were transfected+/-a dominant-negative mutant Akt, treated+/-SF and analysed for gene expression using Affymetrix arrays. These studies identified SF-regulated genes for which induction was c-Akt-dependent vs -independent. Selected microarray findings were confirmed by semiquantitative and quantitative reverse transcription-polymerase chain reaction. We tested the contribution of four SF-inducible/c-Akt-dependent genes (AMPD3, EPHB2, MX1 and WNT4) to protection against adriamycin (a DNA topoisomerase IIalpha inhibitor) using RNA interference. Knockdown of each gene except EPHB2 caused a small but significant reduction in the SF cell protection. The lack of effect of EPHB2 knockdown may be due to the fact that DU-145 cells contain a single-mutant EPHB2 allele. A combination of three small interfering RNAs blocked most of the protection by SF in both DU-145 and T47D cells. These findings identify novel c-Akt-regulated genes, some of which contribute to SF-mediated cytoprotection.

Doxorubicin↗

PubMedDate not supplied

Adaptive double self-organizing maps for clustering gene expression profiles.

This paper introduces a new model of self-organizing map (SOM) known as adaptive double self-organizing map (ADSOM). ADSOM has a flexible topology and performs data partitioning and cluster visualization simultaneously without requiring a priori knowledge about the number of clusters. It combines features of the popular SOM with two-dimensional position vectors, which serve as a visualization tool to detect the number of clusters present in the data. ADSOM updates its free parameters and allows convergence of its position vectors to a fairly consistent number of clusters provided its initial number of nodes is greater than the expected number of clusters. A novel index is introduced based on hierarchical clustering of the final locations of position vectors. The index allows automated detection of the number of clusters, thereby reducing human error that could be incurred from counting clusters visually. To test ADSOM's consistency in data partitioning, we examine the number of common profiles found in the clusters that were obtained by varying the initial number of nodes. This provides a confidence measure for the clusters formed by ADSOM and illustrates the effect of different initial number of nodes on data partitioning. The reliance of ADSOM in identifying number of clusters is demonstrated by applying it to publicly available yeast gene expression data.

Adaptation, Biological↗