Dissecting interferon-induced transcriptional programs in human peripheral blood cells

Interferons are key modulators of the immune system, and are central to the control of many diseases. The response of immune cells to stimuli in complex populations is the product of direct and indirect effects, and of homotypic and heterotypic cell interactions. Dissecting the global transcriptional profiles of immune cell populations may provide insights into this regulatory interplay. The host transcriptional response may also be useful in discriminating between disease states, and in understanding pathophysiology. The transcriptional programs of cell populations in health therefore provide a paradigm for deconvoluting disease-associated gene expression profiles.We used human cDNA microarrays to (1) compare the gene expression programs in human peripheral blood mononuclear cells (PBMCs) elicited by 6 major mediators of the immune response: interferons alpha, beta, omega and gamma, IL12 and TNFalpha; and (2) characterize the transcriptional responses of purified immune cell populations (CD4+ and CD8+ T cells, B cells, NK cells and monocytes) to IFNgamma stimulation. We defined a highly stereotyped response to type I interferons, while responses to IFNgamma and IL12 were largely restricted to a subset of type I interferon-inducible genes. TNFalpha stimulation resulted in a distinct pattern of gene expression. Cell type-specific transcriptional programs were identified, highlighting the pronounced response of monocytes to IFNgamma, and emergent properties associated with IFN-mediated activation of mixed cell populations. This information provides a detailed view of cellular activation by immune mediators, and contributes an interpretive framework for the definition of host immune responses in a variety of disease settings

Decision analytic model for evaluation of suspected coronary disease with stress testing and coronary CT angiography.

RATIONALE AND OBJECTIVES: The aim of this study was to apply a decision analytic model for the evaluation of coronary artery disease (CAD) to define the optimal utilization of coronary computed tomographic angiography (cCTA) and stress testing. MATERIALS AND METHODS: The model tested in this study assumes that CAD is evaluated with a stress test and/or cCTA and that a patient with positive evaluation results undergoes cardiac catheterization. On the basis of values of sensitivity, specificity, and radiation dose from the published literature and test costs from the Medicare fee schedule, a decision tree model was constructed as a function of disease prevalence. RESULTS: The false-negative rate is lowest when cCTA is used as an isolated test. The false-positive rate is minimized when cCTA is used in combination with stress echocardiography. Effective radiation is minimized by use of stress electrocardiography or stress echocardiography alone or prior to cCTA. When the pretest probability of CAD is low, a strategy that uses stress echocardiography followed by cCTA minimizes the false-positive rate and effective radiation exposure, with relatively low imaging costs and with a false-negative rate only slightly higher than a strategy including stress myocardial scintigraphy. As the pretest probability of CAD increases above 20%, the false-negative rate of stress echocardiography followed by cCTA increases by \u3e5% relative to cCTA alone. CONCLUSION: Effective radiation dose and imaging costs for the workup of CAD may be minimized by an appropriate combination of stress testing and cCTA. A strategy that uses stress echocardiography followed by cCTA is most appropriate for the evaluation of low-risk patients with CAD with a pretest probability \u3c 20%, while cCTA alone may be more appropriate in intermediate-risk patients

Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases

Although the introduction of genome-wide association studies (GWAS) have greatly increased the number of genes associated with common diseases, only a small proportion of the predicted genetic contribution has so far been elucidated. Studying the cumulative variation of polymorphisms in multiple genes acting in functional pathways may provide a complementary approach to the more common single SNP association approach in understanding genetic determinants of common disease. We developed a novel pathway-based method to assess the combined contribution of multiple genetic variants acting within canonical biological pathways and applied it to data from 14,000 UK individuals with 7 common diseases. We tested inflammatory pathways for association with Crohn's disease (CD), rheumatoid arthritis (RA) and type 1 diabetes (T1D) with 4 non-inflammatory diseases as controls. Using a variable selection algorithm, we identified variants responsible for the pathway association and evaluated their use for disease prediction using a 10 fold cross-validation framework in order to calculate out-of-sample area under the Receiver Operating Curve (AUC). The generalisability of these predictive models was tested on an independent birth cohort from Northern Finland. Multiple canonical inflammatory pathways showed highly significant associations (p 10−3–10−20) with CD, T1D and RA. Variable selection identified on average a set of 205 SNPs (149 genes) for T1D, 350 SNPs (189 genes) for RA and 493 SNPs (277 genes) for CD. The pattern of polymorphisms at these SNPS were found to be highly predictive of T1D (91% AUC) and RA (85% AUC), and weakly predictive of CD (60% AUC). The predictive ability of the T1D model (without any parameter refitting) had good predictive ability (79% AUC) in the Finnish cohort. Our analysis suggests that genetic contribution to common inflammatory diseases operates through multiple genes interacting in functional pathways

Mandoline: robust cut-cell generation for arbitrary triangle meshes

Although geometry arising "in the wild" most often comes in the form of a surface representation, a plethora of geometrical and physical applications require the construction of volumetric embeddings either of the geometry itself or the domain surrounding it. Cartesian cut-cell-based mesh generation provides an attractive solution in which volumetric elements are constructed from the intersection of the input surface geometry with a uniform or adaptive hexahedral grid. This choice, especially common in computational fluid dynamics, has the potential to efficiently generate accurate, surface-conforming cells; unfortunately, current solutions are often slow, fragile, or cannot handle many common topological situations. We therefore propose a novel, robust cut-cell construction technique for triangle surface meshes that explicitly computes the precise geometry of the intersection cells, even on meshes that are open or non-manifold. Its fundamental geometric primitive is the intersection of an arbitrary segment with an axis-aligned plane. Beginning from the set of intersection points between triangle mesh edges and grid planes, our bottom-up approach robustly determines cut-edges, cut-faces, and finally cut-cells, in a manner designed to guarantee topological correctness. We demonstrate its effectiveness and speed on a wide range of input meshes and grid resolutions, and make the code available as open source.This work is graciously supported by NSERC Discovery Grants (RGPIN-04360-2014 & RGPIN-2017-05524), NSERC Accelerator Grant (RGPAS-2017-507909), Connaught Fund (503114), and the Canada Research Chairs Program

RNA-SeQC: RNA-seq metrics for quality control and process optimization

Summary: RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3′/5′ bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis