Combining genome-wide and targeted gene expression profiling in drug discovery: microarrays and real-time PCR

ISG15 is critical in the control of Chikungunya virus infection independent of UbE1L mediated conjugation

Chikungunya virus (CHIKV) is a re-emerging alphavirus that has caused significant disease in the Indian Ocean region since 2005. During this outbreak, in addition to fever, rash and arthritis, severe cases of CHIKV infection have been observed in infants. Challenging the notion that the innate immune response in infants is immature or defective, we demonstrate that both human infants and neonatal mice generate a robust type I interferon (IFN) response during CHIKV infection that contributes to, but is insufficient for, the complete control of infection. To characterize the mechanism by which type I IFNs control CHIKV infection, we evaluated the role of ISG15 and defined it as a central player in the host response, as neonatal mice lacking ISG15 were profoundly susceptible to CHIKV infection. Surprisingly, UbE1L⁻/⁻ mice, which lack the ISG15 E1 enzyme and therefore are unable to form ISG15 conjugates, displayed no increase in lethality following CHIKV infection, thus pointing to a non-classical role for ISG15. No differences in viral loads were observed between wild-type (WT) and ISG15⁻/⁻ mice, however, a dramatic increase in proinflammatory cytokines and chemokines was observed in ISG15⁻/⁻ mice, suggesting that the innate immune response to CHIKV contributes to their lethality. This study provides new insight into the control of CHIKV infection, and establishes a new model for how ISG15 functions as an immunomodulatory molecule in the blunting of potentially pathologic levels of innate effector molecules during the host response to viral infection.

In vitro end points for the assessment of cellular immune response-modulating drugs

BACKGROUND

The concept of immunotoxicology and the development of a battery of immune-function assays to screen potential immunotoxic compounds have been increasingly used in the past. Immunotoxic outcome generally seems appropriate to evaluate the risk in drug development. Improving this approach is possible, by using methods now available, to study the effect of a chemical compound on the immune system.

OBJECTIVE

The goal of this review is to provide an overview of the current and recent methodologies for testing the immunological effect and immunotoxic risks in drug candidates.

METHODS

The methodological details here discussed include a synthetic description of the immunocompetent cells in cell-mediated immunity and the choice of the most appropriate assay (bioassays, immunoassays, molecular biology techniques, flow cytometry).

CONCLUSION

This review offers an assessment of in vitro models to study the toxic impact of (bio)pharmaceuticals on cellular immune system and aid drug scientists in understanding the significance and the methods to approach immunotoxicology.

Hybridization probe pairs and single-labeled probes: an alternative approach for genotyping and quantification

Real-time polymerase chain reaction (PCR) has become a standard tool in both quantitative gene expression and genetic variation analysis. Data collection is performed throughout the PCR process, thus combining amplification and detection into a single step. This can be achieved by combining a variety of different fluorescent chemistries that correlate the concentration of an amplified PCR product to changes in fluorescence intensity. Hybridization probe pairs and single-labeled probes are sequence-specific, dye-labeled oligonucleotides, used in real-time PCR approaches, in particular for genotyping of single nucleotide polymorphisms (SNPs). In that case, a detector probe is designed to cover the polymorphism. Allelic variants are identified and differentiated via post-PCR melting curve analysis. A single melting curve can distinguish different T (m)s, and differently labeled probes may be used, theoretically allowing multiplexed genotyping of several SNPs.

Uncharacterized/hypothetical proteins in biomedical 'omics' experiments: is novelty being swept under the carpet?

Many 'omics' studies, gene expression microarray experiments in particular, aim at charting the molecular mechanisms of physiology, disease and drug response. This short review discusses the bias present in many such studies whereas the focus is set on the well understood and established molecular scenarios. The under-reporting rate of 'hypothetical' or uncharacterized genes and proteins, differentially regulated in disease context, is assessed here. Reasons for this bias are discussed. Particular examples from the genomics studies on respiratory diseases are presented. This review aims at increasing awareness of the unexplored genomics data and proposes remedies in order to refocus genomics studies on the less-charted territories of the genome, transcriptome and proteome. It is suggested that routine use of function prediction methods in conjunction with omics analyses may allow better interpretation of the data, and facilitate discovery of true novelty.

Prospective use of CYP pharmacogenetics and medication analysis to facilitate improved therapy - a pilot study

OBJECTIVES

To assess the efficacy of cytochrome P450 (CYP) pharmacogenetic testing and medication interaction analysis in a controlled environment for reduction of events, stays in hospital, extra care and required extra doctors visits to the patients.

METHODS

A prospective cohort study of 28 patients in a geriatric care facility with multimedication and at least one report of an event was performed over a period of 7 months. In the first phase of the study the patients were closely monitored twice a day by the care staff, recording all potential events, regardless of association with the indication or not, requirement for extra care, requirement for an unplanned site visit from a physician and days in hospital. In a 1-month period, the patients were genotyped for the cytochromes CYP2C9, CYP2C19 and CYP2D6, and their medication analyzed for interactions, using a proprietary computer program. Recommendations for medication change based upon genetics and/or medication interaction analysis were made to the care physicians. In a second 3-month phase the patients were monitored as in Phase I. The data comparing Phase I with Phase II was analyzed using two way ANOVA.

RESULTS

Of the 28 patients in the study in both phases, 16 (55%) had genetic and/or medication interaction problems that required change of medication. A total of 11 out of 16 (69%) of the patients did have their medication altered by the care physician. Of the 11 patients, five (45%) demonstrated some betterment in the number of reported events after alteration of their medication. Of these five patients, three had improvements when their medication was altered for their genetics. A further three (one patient had improvements due to both effects) had improvements when their medication was altered after a medication interaction analysis.

CONCLUSION

Although an exploratory pilot study, this cohort study shows the possibilities and potential of pharmacogenetic testing for CYP alterations combined with medication interaction analysis of patients in a geriatric care facility.

Enantiomeric separation and determination of absolute stereochemistry of asymmetric molecules in drug discovery—Building chiral technology toolboxes

The application of Chiral Technology, or the (extensive) use of techniques or tools for the determination of absolute stereochemistry and the enantiomeric or chiral separation of racemic small molecule potential lead compounds, has been critical to successfully discovering and developing chiral drugs in the pharmaceutical industry. This has been due to the rapid increase over the past 10-15 years in potential drug candidates containing one or more asymmetric centers. Based on the experiences of one pharmaceutical company, a summary of the establishment of a Chiral Technology toolbox, including the implementation of known tools as well as the design, development, and implementation of new Chiral Technology tools, is provided.

Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR

Quantitative real-time PCR (qPCR) is a commonly used validation tool for confirming gene expression results obtained from microarray analysis; however, microarray and qPCR data often result in disagreement. The current study assesses factors contributing to the correlation between these methods in five separate experiments employing two-color 60-mer oligonucleotide microarrays and qPCR using SYBR green. Overall, significant correlation was observed between microarray and qPCR results (ρ=0.708, p<0.0001, n=277) using these platforms. The contribution of factors including up- vs. down-regulation, spot intensity, ρ-value, fold-change, cycle threshold (C_t), array averaging, tissue type, and tissue preparation was assessed. Filtering of microarray data for measures of quality (fold-change and ρ-value) proves to be the most critical factor, with significant correlations of ρ>0.80 consistently observed when quality scores are applied.

INTEGRATION OF NANOPARTICLES WITH PROTEIN MICROARRAYS

A variety of DNA, protein or cell microarray devices and systems have been developed and commercialized. In addition to the biomolecule related analysis, they are also being used for pharmacogenomic research, infectious and genetic disease and cancer diagnostics, and proteomic and cellular analysis.1 Currently, microarray is fabricated on a planar surface; this limits the amount of biomolecules that can be bounded on the surface. In this work, a planar protein microarray chip with nonplanar spot surface was fabricated to enhance the chip performance. A nonplanar spot surface was created by first coating the silica nanoparticles with albumin and depositing them into the patterned microwells. The curve surfaces of the nanoparticles increase the surface area for immobilization of proteins, which helps to enhance the detection sensitivity of the chip. Using this technique, proteins are immobilized onto the nanoparticles before they are deposited onto the chip, and therefore the method of protein immobilization can be customized at each spot. Furthermore, a nonplanar surface promotes the retention of native protein structure better than planar surface.2 The technique developed can be used to produce different types of microarrays, such as DNA, protein and antibody microarrays.

Establishment of a real-time PCR protocol for expression studies of secondary metabolite biosynthetic gene clusters in the G/C-rich myxobacterium Sorangium cellulosum So ce56

In the attempt to establish a reliable real-time PCR protocol for transcriptional analysis of secondary metabolism in Sorangium cellulosum strain So ce56, a RNA extraction method and a reverse transcription protocol was developed. In order to validate chivosazol or etnangien gene cluster transcripts as good candidates to develop the real-time PCR protocol, stability measurements of the transcripts were performed proving both transcripts to be very stable. The chivosazol biosynthetic gene cluster was taken as the test case to evaluate the special problems arising from the large size of the transcripts and the high G/C-content of the encoding DNA. A set of primer pairs targeting the presumed 90 kbp chivosazol transcript at different positions was employed. The production rate of chivosazol was compared to the transcription of the operon in time course experiments revealing that during the logarithmic growth phase transcription is maximally induced and levels out during the stationary phase. Some deviations in transcript numbers could be measured depending on the primer pair used, but cross-evaluation strengthened the notion that the measured numbers reflect the whole transcript quantities and the in vivo level. Finally, a putative promoter located between chiA and chiB was examined by using the developed real-time PCR protocol.

The power of real-time PCR

In recent years, real-time polymerase chain reaction (PCR) has emerged as a robust and widely used methodology for biological investigation because it can detect and quantify very small amounts of specific nucleic acid sequences. As a research tool, a major application of this technology is the rapid and accurate assessment of changes in gene expression as a result of physiology, pathophysiology, or development. This method can be applied to model systems to measure responses to experimental stimuli and to gain insight into potential changes in protein level and function. Thus physiology can be correlated with molecular events to gain a better understanding of biological processes. For clinical molecular diagnostics, real-time PCR can be used to measure viral or bacterial loads or evaluate cancer status. Here, we discuss the basic concepts, chemistries, and instrumentation of real-time PCR and include present applications and future perspectives for this technology in biomedical sciences and in life science education.

Recent advances in microarrays

An overview is presented for the current DNA-based microarray market, including applications for microarrays in areas such as gene expression, single-nucleotide polymorphism, strain differentiation, de novo DNA synthesis, aptamers and advances in 'in situ' synthesis technology. The development of new detection methods, simplified methodologies and broad application to molecular diagnostics are rapidly migrating microarray technologies into the arena of diagnostics and personalized medicine. Comparisons of microarray technologies from various manufacturers are presented.: