Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes.

Gene expression signatures of toxicity and clinical response benefit both safety assessment and clinical practice; however, difficulties in connecting signature genes with the predicted end points have limited their application. The Microarray Quality Control Consortium II (MAQCII) project generated 262 signatures for ten clinical and three toxicological end points from six gene expression data sets, an unprecedented collection of diverse signatures that has permitted a wide-ranging analysis on the nature of such predictive models. A comprehensive analysis of the genes of these signatures and their nonredundant unions using ontology enrichment, biological network building and interactome connectivity analyses demonstrated the link between gene signatures and the biological basis of their predictive power. Different signatures for a given end point were more similar at the level of biological properties and transcriptional control than at the gene level. Signatures tended to be enriched in function and pathway in an end point and model-specific manner, and showed a topological bias for incoming interactions. Importantly, the level of biological similarity between different signatures for a given end point correlated positively with the accuracy of the signature predictions. These findings will aid the understanding, and application of predictive genomic signatures, and support their broader application in predictive medicine.

Regulation of Ca2+ release by cAMP-dependent protein kinase. A mechanism for agonist-specific calcium signaling?

Calcium is an ubiquitous second messenger that is involved in the regulation of a number of cell functions. The mechanism by which the specificity of calcium signaling is achieved is not well understood. We suggest that calcium release from the ER can occur selectively at different spatial locations in response to different extracellular stimuli. We discuss a possible mechanism for such selectivity and present a model based on this mechanism. The suggested mechanism is based on the regulation of local Ca2+ release by cyclic AMP-dependent protein kinase (PKA) and relies upon two experimental observations: first, some G-protein coupled signaling pathways activate PLC and regulate adenylate cyclase at the same time, leading to IP3 production and altering PKA activity via changes in cAMP level; second, phosphorylation by PKA alters the properties of IP3 receptor (IP3R). In our model we consider allosteric regulation of IP3Rs by IP3 and cAMP-dependent phosphorylation. The differences in IP3Rs and PKA densities at different spatial locations within the cell allow the release of calcium selectively at each location in response to certain combination of IP3 and cAMP concentration. Specificity of agonist-response coupling is achieved if different combinations in the levels of these second messengers are specific for different extracellular stimuli.

Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms.

The authors have previously applied two integrated platforms, MetaCore and MetaDrug, for the assembly and analysis of human biological networks as a useful method for the integration and functional interpretation of high-throughput experimental data. The present study demonstrates in detail the specific algorithms that are used in both software platforms. Using a standard set of genes as input, namely CYP3A4 (an enzyme), PXR (a nuclear hormone receptor), MDR1 (a transporter) and hERG (an ion channel) related to the absorption, distribution, metabolism, excretion and toxicity (ADME/Tox) of xenobiotics, we have now generated networks with each algorithm. The relative advantages and disadvantages of these algorithms are explained using these examples as well as appropriate instances of utility to illustrate further the particular circumstances for their use. In addition, the benefits of the different network algorithms are identified when compared with algorithms available in other products, where this information is available.

Calcium waves in a model with a random spatially discrete distribution of Ca2+ release sites.

We study the propagation of intracellular calcium waves in a model that features Ca2+ release from discrete sites in the endoplasmic reticulum membrane and random spatial distribution of these sites. The results of our simulations qualitatively reproduce the experimentally observed behavior of the waves. When the level of the channel activator inositol trisphosphate is low, the wave undergoes fragmentation and eventually vanishes at a finite distance from the region of initiation, a phenomenon we refer to as an abortive wave. With increasing activator concentration, the mean distance of propagation increases. Above a critical level of activator, the wave becomes stable. We show that the heterogeneous distribution of Ca2+ channels is the cause of this phenomenon.

Calcium influx factor is synthesized by yeast and mammalian cells depleted of organellar calcium stores.

Depletion of endoplasmic reticulum Ca2+ stores leads to the entry of extracellular Ca2+ into the cytoplasm, a process termed capacitative or store-operated Ca2+ entry. Partially purified extracts were prepared from the human Jurkat T lymphocyte cell line and yeast in which Ca2+ stores were depleted by chemical and genetic means, respectively. After microinjection into Xenopus laevis oocytes, the extracts elicited a wave of increased cytoplasmic free Ca2+ ([Ca2+]i) that spread from the point of injection across the oocyte. Extracts from cells with replete organellar Ca2+ stores were inactive. The increases depended on extracellular Ca2+, were unaffected by the inositol 1,4,5-trisphosphate (IP3) inhibitor heparin or an anti-IP3 receptor antibody and were unchanged when the endoplasmic reticulum was segregated to the hemisphere opposite the injection site by centrifugation. Confocal microscopy revealed that [Ca2+]i increases were most pronounced at the periphery of the oocyte. The patterns of [Ca2+]i increases were replicated by computer simulations based on a diffusible messenger of about 700 Da that directly activates Ca2+ influx. In addition, ICRAC, a Ca2+ release-activated Ca2+ current monitored in Jurkat cells by whole-cell patch clamp recordings, was more rapidly activated when active extracts were included in the patch pipette than by the inclusion of a Ca2+ chelator or IP3. These data support the existence in yeast and mammalian cells depleted of Ca2+ stores of a functionally conserved diffusible calcium influx factor that directly activates Ca2+ influx.