An adaptation of the LMS method to determine expression variations in profiling data

One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expression variation (EV), based on the LMS method, which allows data normalization and to construct confidence bands of gene expression, fitting cubic spline curves to the Box-Cox transformation. The confidence bands, fitted to the actual variance of the data, include the genes devoid of significant variation, and allow, based on the confidence bandwidth, to calculate EVs. Each outlier is positioned according to the dispersion space (DS) and a P-value is statistically calculated to determine EV. This model results in variance stabilization. Using two Affymetrix-generated datasets, the sets of differentially expressed genes selected using EV and other classical methods were compared. The analysis suggests that EV is more robust on variance stabilization and on selecting differential expression from both rare and strongly expressed genes.     

Novel anticancer drug discovery.

There is at present, much optimism about the possibility of finding selective anticancer drugs that will eliminate the cytotoxic side effects associated with conventional cancer chemotherapy. This hope is based on uncovering many novel molecular targets that are 'cancer-specific', which will allow the targeting of cancer cells while normal cells are spared. Thus far, encouraging results have been obtained with several of these novel agents at the preclinical level, and clinical trials have begun. These targets are involved at one level or more in tumor biology, including tumor cell proliferation, angiogenesis and metastasis. Novel targets for which advances are being made include the following: growth factor receptor tyrosine kinases such as the epidermal growth factor receptor and HER-2/neu (proliferation); the vascular endothelial growth factor receptor and the basic fibroblast growth factor receptor (angiogenesis); the oncogenic GTP-binding protein Ras (especially agents targeting Ras farnesylation, farnesyltransferase inhibitors) (proliferation); protein kinase C (proliferation and drug resistance); cyclin-dependent kinases (proliferation); and matrix metalloproteinases and angiogenin (angiogenesis and metastasis). Less explored, but potentially useful targets include the receptor tyrosine kinase platelet-derived growth factor receptor, mitogen-activated protein kinase cascade oncogenes such as Raf-1 and mitogen-activated protein kinase kinase, cell adhesion molecules such as integrins, anti-apoptosis proteins such as Bcl-2, MDM2 and survivin, and the cell life-span target telomerase.     

Apoptosis and anticancer drug resistance.

Anticancer agents induce cancer cell death through apoptosis or necrosis. As anticancer agents at low and high concentrations cause apoptosis and necrosis, respectively, cancer cells may be merely injured by an anticancer agent in apoptosis, and cell death may result from an activation of the internal constituents to induce apoptosis. Therefore, an alternation of apoptotic pathway must change the efficacy of anticancer agents. As an escape of cancer cells from apoptosis seems to be closely associated with the development of anticancer resistance, this report focuses on mechanisms of apoptosis and its association with anticancer resistance. A Bax induces apoptosis mitochondria-dependently, whereas Fas can induce apoptosis mitochondria-independently. An interaction of Bax and Bcl-2 is very important to decide cell life or death, and Bcl-2 phosphorylation may control this interaction: Paclitaxel treatment induced Bcl-2 phosphorylation and typical apoptosis, whereas hyperthermia induced not Bcl-2 phosphorylation but nuclear translocation and failed to induce apoptosis. Moreover, Fas was localized in the cytoplasm of exponentially growing cells and on the cell membrane of confluent cells. We would like to emphasize that it is very important to check the localization of constituents of apoptosis in order to evaluate the susceptibility of cancer cells to apoptosis.     

A novel platform for accelerated pharmacodynamic profiling for lead optimization of anticancer drug candidates

Oncology drug discovery is, by definition, a target-rich enterprise. High-throughput screening (HTS) laboratories have supported a wide array of molecularly targeted and chemical genomic approaches for anticancer lead generation, and the number of hits emerging from such campaigns has increased dramatically. Although automation of HTS processes has eliminated primary screening as a bottleneck, the demands on secondary screening in appropriate cell-based assays have increased concomitantly with the numbers of hits delivered to therapeutic area laboratories. The authors describe herein the implementation of a novel platform using off-the-shelf solutions that have allowed them to efficiently characterize hundreds of HTS hits using a palette of Western blot-based pharmacodynamic assays. The platform employs a combination of a flatbed bufferless SDS-PAGE system, a dry ultra-rapid electroblotting apparatus, and a highly sensitive and quantitative infrared imaging system. Cumulatively, this platform has significantly reduced the cycle time for HTS hit evaluation. In addition, the routine use of this platform has resulted in higher quality data that have allowed the development of structure-activity databases that have tangibly improved lead optimization. The authors describe in detail the application of this platform, designated the Accelerated Pharmaco-Dynamic Profiler (APDP), to the annotation of inhibitors of 2 attractive oncology targets, BRAF kinase and Hsp90.     

Gene expression profiling and its practice in drug development

The availability of sequenced genomes of human and many experimental animals necessitated the development of new technologies and powerful computational tools that are capable of exploiting these genomic data and ask intriguing questions about complex nature of biological processes. This gave impetus for developing whole genome approaches that can produce functional information of genes in the form of expression profiles and unscramble the relationships between variation in gene expression and the resulting physiological outcome. These profiles represent genetic fingerprints or catalogue of genes that characterize the cell or tissue being studied and provide a basis from which to begin an investigation of the underlying biology. Among the most powerful and versatile tools are high-density DNA microarrays to analyze the expression patterns of large numbers of genes across different tissues or within the same tissue under a variety of experimental conditions or even between species. The wide spread use of microarray technologies is generating large sets of data that is stimulating the development of better analytical tools so that functions can be predicted for novel genes. In this review, the authors discuss how these profiles are being used at various stages of the drug discovery process and help in the identification of new drug targets, predict the function of novel genes, and understand individual variability in response to drugs.     

Chemoproteomic approaches to drug target identification and drug profiling

Chemoproteomics represents a new research discipline at the interface of medicinal chemistry, biochemistry, and cell biology focused on studying the molecular mechanisms of action of drugs and other bioactive small molecules. Research strategies frequently combine phenotypic screening with subsequent target identification, and aim at a proteome-wide characterization of drug-induced changes in cellular protein expression and post-translational modifications. In recent years quantitative mass spectrometry has taken center stage in many of these approaches. This review describes experimental strategies in current chemical proteomics research, discusses recent examples of successful applications, and highlights areas in drug discovery where chemical proteomics-based assays using native endogenous proteins are expected to have substantial impact.     

Characterization of DNA reactive and non-DNA reactive anticancer drugs by gene expression profiling

Gene expression profiling technology is expected to advance our understanding of genotoxic mechanisms involving direct or indirect interaction with DNA. We exposed human lymphoblastoid TK6 cells to 14 anticancer drugs (vincristine, paclitaxel, etoposide, daunorubicin, camptothecin, amsacrine, cytosine arabinoside, hydroxyurea, methotrexate, 5-fluorouracil, cisplatin, 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea (CCNU), 1,3-bis (2-chloroethyl)-1-nitrosourea (BCNU), and bleomycin) for 4-h and examined them immediately or after a 20-h recovery period. Cytotoxicity and genotoxicity, respectively, were evaluated by cell counting and by in vitro micronucleus assay at 24h. Effects on the cell cycle were determined by flow cytometry at 4 and 24h. Gene expression was profiled at both sampling times by using human Affymetrix U133A GeneChips (22K). Bioanalysis was done with Resolver/Rosetta software and an in-house annotation program. Cell cycle analysis and gene expression profiling allowed us to classify the drugs according to their mechanisms of action. The molecular signature is composed of 28 marker genes mainly involved in signal transduction and cell cycle pathways. Our results suggest that these marker genes could be used as a predictive model to classify genotoxins according to their direct or indirect interaction with DNA.     

Quantitative mRNA expression profiling of heat-shock protein families in rainbow trout cells

We isolated multiple HSPs from rainbow trout Oncorhynchus mykiss RTG-2 cells and quantitatively compared their mRNA levels between unstressed and heat-shocked cells using real-time RT-PCR analysis. Consequently, we isolated nine cDNAs encoding HSPs from heat-shocked RTG-2 cells, namely, Hsp90betaa, Hsp90betab, Grp78, Hsp70a, Hsc70a, Hsc70b, Cct8, Hsp47, and DnaJ homolog. Quantitative RT-PCR analyses, in which Hsp70b isolated previously was included, showed that the mRNA accumulation levels of Hsp70a, Hsp70b, Hsc70a, Hsc70b, and Hsp47 were significantly increased after heat shock, and the increased levels of two Hsp70s, Hsp70a, and Hsp70b, were most conspicuous. In the case of Hsc70s, the increased level of Hsc70b was more remarkable than that of Hsc70a. These results demonstrate the importance of a comprehensive expression analysis of HSPs for better understanding of the cellular stress response in fish, especially in tetraploid species such as rainbow trout.     

Global expression profiling applied to plant development

Plant development is controlled by both endogenous genetic programs and responses to exogenous signals. Microarray experiments are being used to identify the genes involved in these developmental processes. Most of the analyses conducted to date have been conducted on whole organs. Although these studies have provided valuable information, they are limited by the composite nature of plant organs that consist of multiple cell types. Technical advances that have made it possible to study global patterns of gene expression in individual cell types promise to increase greatly the information revealed by microarray experiments.     

Using a nonrecursive formula to determine cladogram probabilities

Three properties of bifurcating branching diagrams that are used for representing a specific number of taxa are (1) the number of possible arrangements, (2) the number of possible topologies, and (3) the probabilities of formation according to particular models of cladogenesis. Of these, the probabilities have received the least attention in the literature. Indeed, many biologists would be astonished by the observation that the probability of a commonly cited cladogram containing 35 phyla of the animal kingdom is < 0.0072% of the value of the average probability taken over all possible cladograms! We reviewed works on cladogram arrangements and topologies and developed a computer-generated table of enumerations that extends and corrects such tables in the literature. We also developed a nonrecursive formula for the determination of cladogram probabilities. This formula facilitates calculation and thereby should promote use of cladogram probabilities, which might provide more accurate null hypotheses for tests of cladogenic events than do considerations of cladogram arrangements or topologies.     

Oxfendazole: regimen-dependent expression of drug efficacy against Trichinella spiralis

An investigation of the chemotherapeutic effectiveness of a new broad-spectrum anthelmintic, oxfendazole (OXF, methyl 5[6]-phenylsulfinyl-2-benzimidazolecarbamate), against Trichinella spiralis is reported. OXF was highly effective against adult T. spiralis in mice subjected to a 4-day course of treatment during the enterai phase of experimental trichinellosis. When treatment began 72 h after the mice were inoculated with parasites, the number of adult worms recovered from the host intestine was greatly reduced by twice-daily oral doses of OXF at 12.5 mg/kg body wt. The same dosage regimen (12.5 mg/kg bis in die) was also highly effective against the muscle-dwelling larvae of T. spiralis when given on 4 successive days during the invasive (days 14–17) and encystment phases (days 28–31) of infection.     

Robust ordered mRNA differential display: an improved method for global gene expression profiling

Global gene expression profiling (GGEP) plays a pivotal role in biological research. We developed an improved GGEP method called "robust ordered mRNA differential display (RoDD)" by combining mRNA differential display (DD) and complementary DNA amplified fragment length polymorphisms (cDNA-AFLP) using elaborately designed primers and a poly (dT:A) replacement technique. Redundancy was minimized by bead-based isolation and coverage was improved by using restriction enzymes that recognized 4-bp sites. This method offers the common virtues of gel-based methods along with the reliability of cDNA-AFLP. The most significant advantage of RoDD over current gel-based methods is greatly improved coverage and minimized redundancy.