Management of platelet-directed pharmacotherapy in patients with atherosclerotic coronary artery disease undergoing elective endoscopic gastrointestinal procedures.

The periprocedural management of patients with atherosclerotic coronary heart disease, including those who have heart disease and those who are undergoing percutaneous coronary intervention and stent placement who might require temporary interruption of platelet-directed pharmacotherapy for the purpose of an elective endoscopic gastrointestinal procedure, is a common clinical scenario in daily practice. Herein, we summarize the available information that can be employed for making management decisions and provide general guidance for risk assessment.

Effect of various normalization methods on Applied Biosystems expression array system data.

BACKGROUND: DNA microarray technology provides a powerful tool for characterizing gene expression on a genome scale. While the technology has been widely used in discovery-based medical and basic biological research, its direct application in clinical practice and regulatory decision-making has been questioned. A few key issues, including the reproducibility, reliability, compatibility and standardization of microarray analysis and results, must be critically addressed before any routine usage of microarrays in clinical laboratory and regulated areas can occur. In this study we investigate some of these issues for the Applied Biosystems Human Genome Survey Microarrays. RESULTS: We analyzed the gene expression profiles of two samples: brain and universal human reference (UHR), a mixture of RNAs from 10 cancer cell lines, using the Applied Biosystems Human Genome Survey Microarrays. Five technical replicates in three different sites were performed on the same total RNA samples according to manufacturer's standard protocols. Five different methods, quantile, median, scale, VSN and cyclic loess were used to normalize AB microarray data within each site. 1,000 genes spanning a wide dynamic range in gene expression levels were selected for real-time PCR validation. Using the TaqMan assays data set as the reference set, the performance of the five normalization methods was evaluated focusing on the following criteria: (1) Sensitivity and reproducibility in detection of expression; (2) Fold change correlation with real-time PCR data; (3) Sensitivity and specificity in detection of differential expression; (4) Reproducibility of differentially expressed gene lists. CONCLUSION: Our results showed a high level of concordance between these normalization methods. This is true, regardless of whether signal, detection, variation, fold change measurements and reproducibility were interrogated. Furthermore, we used TaqMan assays as a reference, to generate TPR and FDR plots for the various normalization methods across the assay range. Little impact is observed on the TP and FP rates in detection of differentially expressed genes. Additionally, little effect was observed by the various normalization methods on the statistical approaches analyzed which indicates a certain robustness of the analysis methods currently in use in the field, particularly when used in conjunction with the Applied Biosystems Gene Expression System.

Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays.

BACKGROUND: DNA microarrays are rapidly becoming a fundamental tool in discovery-based genomic and biomedical research. However, the reliability of the microarray results is being challenged due to the existence of different technologies and non-standard methods of data analysis and interpretation. In the absence of a "gold standard"/"reference method" for the gene expression measurements, studies evaluating and comparing the performance of various microarray platforms have often yielded subjective and conflicting conclusions. To address this issue we have conducted a large scale TaqMan Gene Expression Assay based real-time PCR experiment and used this data set as the reference to evaluate the performance of two representative commercial microarray platforms. RESULTS: In this study, we analyzed the gene expression profiles of three human tissues: brain, lung, liver and one universal human reference sample (UHR) using two representative commercial long-oligonucleotide microarray platforms: (1) Applied Biosystems Human Genome Survey Microarrays (based on single-color detection); (2) Agilent Whole Human Genome Oligo Microarrays (based on two-color detection). 1,375 genes represented by both microarray platforms and spanning a wide dynamic range in gene expression levels, were selected for TaqMan Gene Expression Assay based real-time PCR validation. For each platform, four technical replicates were performed on the same total RNA samples according to each manufacturer's standard protocols. For Agilent arrays, comparative hybridization was performed using incorporation of Cy5 for brain/lung/liver RNA and Cy3 for UHR RNA (common reference). Using the TaqMan Gene Expression Assay based real-time PCR data set as the reference set, the performance of the two microarray platforms was evaluated focusing on the following criteria: (1) Sensitivity and accuracy in detection of expression; (2) Fold change correlation with real-time PCR data in pair-wise tissues as well as in gene expression profiles determined across all tissues; (3) Sensitivity and accuracy in detection of differential expression. CONCLUSION: Our study provides one of the largest "reference" data set of gene expression measurements using TaqMan Gene Expression Assay based real-time PCR technology. This data set allowed us to use an alternative gene expression technology to evaluate the performance of different microarray platforms. We conclude that microarrays are indeed invaluable discovery tools with acceptable reliability for genome-wide gene expression screening, though validation of putative changes in gene expression remains advisable. Our study also characterizes the limitations of microarrays; understanding these limitations will enable researchers to more effectively evaluate microarray results in a more cautious and appropriate manner.

Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates.

The high degree of sequence similarity between human and nonhuman primate (NHP) genomic DNA suggests that human genome sequence-based DNA microarrays may be used effectively to study gene expression in NHP disease models. In the present study, two distinct commercially available human genome microarray platforms, the Affymetrix HG U133A GeneChip System utilizing Human Genome U133A GeneChips and the Applied Biosystems Expression Array System utilizing the Human Genome Survey Microarray, were used to identify and characterize gene expression changes in the anterior cerebellum of a macaque monkey model of human alcoholism. The Affymetrix microarray consists of eleven short oligonucleotide probe sets for each gene while the Applied Biosystems Microarray uses a single long oligonucleotide per gene. Cross-mapping of probes revealed a total of 11,542 genes that are represented on both microarray platforms. Absolute measures of gene expression ("present calls") from the cerebellum RNA samples were 65-70% (Applied Biosystems Expression Array System) and 27-30% (AffymetrixGeneChip System) among these common gene targets. Analysis of variance (ANOVA; p<0.05; >1.2 fold change; detected on at least 50% of the arrays) indicated 932 and 515 differentially expressed genes for the Applied Biosystems and Affymetrix microarrays, respectively. Significance analysis of microarrays (SAM) identified 255 significant genes at 5% false discovery rate (FDR) for the Applied Biosystems data set and five significant genes at 60% FDR (minimum FDR) for the Affymetrix data set. TaqMan assay-based real-time PCR validation of a number of differentially-expressed genes yielded results that agreed well with the array data in the majority of comparisons. This study demonstrates that human sequence-based DNA arrays can be used effectively to detect differential gene expression in an NHP disease model and provides evidence that the use of this long oligonucleotide-based microarray platform may be more suitable for cross-species gene expression studies than a short oligonucleotide-based system.

Management of platelet-directed pharmacotherapy in patients with atherosclerotic coronary artery disease undergoing elective endoscopic gastrointestinal procedures.

The periprocedural management of patients with atherosclerotic coronary heart disease, including those who have heart disease and those who are undergoing percutaneous coronary intervention and stent placement who might require temporary interruption of platelet-directed pharmacotherapy for the purpose of an elective endoscopic gastrointestinal procedure, is a common clinical scenario in daily practice. Herein, we summarize the available information that can be employed for making management decisions and provide general guidance for risk assessment.

The effect of voluntary trunk rotation and half-field eye-patching for patients with unilateral neglect in stroke: a randomized controlled trial.

OBJECTIVE: To investigate the effectiveness of voluntary trunk rotation and half-field eye-patching to treat patients with unilateral neglect in stroke. DESIGN: Pre-post, day 60 follow-up, single-blinded randomized controlled trial. SETTING: Single-centre inpatient rehabilitation hospital. SUBJECTS: Sixty subacute patients with right hemisphere stroke having unilateral neglect within eight weeks post stroke consented to participate between November 2003 and July 2005. They were randomly assigned to three comparison groups. INTERVENTIONS: Nineteen patients received daily experimental training in voluntary trunk rotation (TR) for 1 hour five times a week for 30 days. Twenty patients received the same kind of treatment together with half-field eye-patching (TR + EP). Fifteen patients in the control group received conventional training with the same contact time. MAIN OUTCOME MEASURES: Patients were assessed on days 0, 30 and 60 using the Behavioural Inattention Test, the Clock Drawing Test, and the Functional Independence Measure. RESULTS: No significant differences between voluntary trunk rotation (TR), voluntary trunk rotation and half-field eye-patching (TR + EP) and controls were found in functional performance and neglect measures at day 30 (P = 0.042-0.994) and follow-up (P = 0.052-0.911) at P = 0.005 using Bonferroni correction. CONCLUSIONS: The results of this study do not support the use of voluntary trunk rotation alone or with half-field eye-patching to improve functional performance or reduce unilateral neglect in subacute patients with stroke.

Gene expression signature in peripheral blood detects thoracic aortic aneurysm.

BACKGROUND: Thoracic aortic aneurysm (TAA) is usually asymptomatic and associated with high mortality. Adverse clinical outcome of TAA is preventable by elective surgical repair; however, identifying at-risk individuals is difficult. We hypothesized that gene expression patterns in peripheral blood cells may correlate with TAA disease status. Our goal was to identify a distinct gene expression signature in peripheral blood that may identify individuals at risk for TAA. METHODS AND FINDINGS: Whole genome gene expression profiles from 94 peripheral blood samples (collected from 58 individuals with TAA and 36 controls) were analyzed. Significance Analysis of Microarray (SAM) identified potential signature genes characterizing TAA vs. normal, ascending vs. descending TAA, and sporadic vs. familial TAA. Using a training set containing 36 TAA patients and 25 controls, a 41-gene classification model was constructed for detecting TAA status and an overall accuracy of 78+/-6% was achieved. Testing this classifier on an independent validation set containing 22 TAA samples and 11 controls yielded an overall classification accuracy of 78%. These 41 classifier genes were further validated by TaqMan real-time PCR assays. Classification based on the TaqMan data replicated the microarray results and achieved 80% classification accuracy on the testing set. CONCLUSIONS: This study identified informative gene expression signatures in peripheral blood cells that can characterize TAA status and subtypes of TAA. Moreover, a 41-gene classifier based on expression signature can identify TAA patients with high accuracy. The transcriptional programs in peripheral blood leading to the identification of these markers also provide insights into the mechanism of development of aortic aneurysms and highlight potential targets for therapeutic intervention. The classifier genes identified in this study, and validated by TaqMan real-time PCR, define a set of promising potential diagnostic markers, setting the stage for a blood-based gene expression test to facilitate early detection of TAA.

The involvement of calcineurin in acetylcholine receptor redistribution in muscle.

In this study the intracellular signaling involved in acetylcholine receptor (AChR) redistribution in muscle was investigated. In cultured Xenopus embryonic muscle cells, both the dispersal of preexisting AChR clusters and the induction of new AChR clusters by growth factor-coated polystyrene beads were inhibited by two specific antagonists of the ser/thr phosphatase calcineurin (CaN), Cyclosporin A, (CsA) and FK-506, but not by KN-93 that blocks CaM kinases. Moreover, CaN inhibition decreased AChR clustering in Xenopus muscle cells by beads coated with antibodies that cross-link and activate the agrin receptor MuSK (muscle-specific kinase) and reduced the agrin-induced tyrosine phosphorylation of MuSK in cultured mouse (C2) myotubes. Last, the length and the number of AChR clusters generated by agrin in C2 myotubes were decreased by treatment with CsA, but not KN-93, and following the forced expression of a dominant negative CaN mutant in these cells, but not wild-type CaN or reporter green fluorescent protein. Collectively, our results support a role for CaN signaling in the redistribution of AChRs in muscle induced by synaptogenic signals.