Albert Hsiao

VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data

Microarrays are invaluable high-throughput tools used to snapshot the gene expression profiles of cells and tissues. Among the most basic and fundamental questions asked of microarray data is whether individual genes are significantly activated or repressed by a particular stimulus. We have previously presented two Bayesian statistical methods for this level of analysis, collectively known as variance-modeled posterior inference with regional exponentials (VAMPIRE). These methods each require a sophisticated modeling step followed by integration of a posterior probability density. We present here a publicly available, web-based platform that allows users to easily load data, associate related samples and identify differentially expressed features using the VAMPIRE statistical framework. In addition, this suite of tools seamlessly integrates a novel gene annotation tool, known as GOby, which identifies statistically overrepresented gene groups. Unlike other tools in this genre, GOby can localize enrichment while respecting the hierarchical structure of annotation systems like Gene Ontology (GO). By identifying statistically significant enrichment of GO terms, Kyoto Encyclopedia of Genes and Genomes pathways, and TRANSFAC transcription factor binding sites, users can gain substantial insight into the physiological significance of sets of differentially expressed genes. The VAMPIRE microarray suite can be accessed at .

Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes

MOTIVATION Microarrays are becoming an increasingly common tool for observing changes in gene expression over a large cross section of the genome. This experimental tool is particularly valuable for understanding the genome-wide changes in gene transcription in response to thiazolidinedione (TZD) treatment. The TZD class of drugs is known to improve insulin-sensitivity in diabetic patients, and is clinically used in treatment regimens. In cells, TZDs bind to and activate the transcriptional activity of peroxisome proliferator-activated receptor gamma (PPAR-gamma). Large-scale array analyses will provide some insight into the mechanisms of TZD-mediated insulin sensitization. Unfortunately, a theoretical basis for analyzing array data has not kept pace with the rapid adoption of this tool. The methods that are commonly used, particularly the fold-change approach and the standard t-test, either lack statistical rigor or resort to generalized statistical models that do not accurately estimate variability at low replicate numbers. RESULTS We introduce a statistical framework that models the dependence of measurement variance on the level of gene expression in the context of a Bayesian hierarchical model. We compare several methods of parameter estimation and subsequently apply these to determine a set of genes in 3T3-L1 adipocytes that are differentially regulated in response to TZD treatment. When the number of experimental replicates is low (n = 2-3), this approach appears to qualitatively preserve an equivalent degree of specificity, while vastly improving sensitivity over other comparable methods. In addition, the statistical framework developed here can be readily applied to understand the implicit assumptions made in traditional fold-change approaches to array analysis.

Rapid Pediatric Cardiac Assessment of Flow and Ventricular Volume With Compressed Sensing Parallel Imaging Volumetric Cine Phase-Contrast MRI

OBJECTIVE The quantification of cardiac flow and ventricular volumes is an essential goal of many congenital heart MRI examinations, often requiring acquisition of multiple 2D phase-contrast and bright-blood cine steady-state free precession (SSFP) planes. Scan acquisition, however, is lengthy and highly reliant on an imager who is well-versed in structural heart disease. Although it can also be lengthy, 3D time-resolved (4D) phase-contrast MRI yields global flow patterns and is simpler to perform. We therefore sought to accelerate 4D phase contrast and to determine whether equivalent flow and volume measurements could be extracted. MATERIALS AND METHODS Four-dimensional phase contrast was modified for higher acceleration with compressed sensing. Custom software was developed to process 4D phase-contrast images. We studied 29 patients referred for congenital cardiac MRI who underwent a routine clinical protocol, including cine short-axis stack SSFP and 2D phase contrast, followed by contrast-enhanced 4D phase contrast. To compare quantitative measurements, Bland-Altman analysis, paired Student t tests, and F tests were used. RESULTS Ventricular end-diastolic, end-systolic, and stroke volumes obtained from 4D phase contrast and SSFP were well correlated (ρ = 0.91-0.95; r(2) = 0.83-0.90), with no statistically significant difference. Ejection fractions were well correlated in a subpopulation that underwent higher-resolution compressed-sensing 4D phase contrast (ρ = 0.88; r(2) = 0.77). Four-dimensional phase contrast and 2D phase contrast flow rates were also well correlated (ρ = 0.90; r(2) = 0.82). Excluding ventricles with valvular insufficiency, cardiac outputs derived from outlet valve flow and stroke volumes were more consistent by 4D phase contrast than by 2D phase contrast and SSFP. CONCLUSION Combined parallel imaging and compressed sensing can be applied to 4D phase contrast. With custom software, flow and ventricular volumes may be extracted with comparable accuracy to SSFP and 2D phase contrast. Furthermore, cardiac outputs were more consistent by 4D phase contrast.

Venous and arterial flow quantification are equally accurate and precise with parallel imaging compressed sensing 4D phase contrast MRI.

To evaluate the precision and accuracy of parallel‐imaging compressed‐sensing 4D phase contrast (PICS‐4DPC) magnetic resonance imaging (MRI) venous flow quantification in children with patients referred for cardiac MRI at our childrens hospital.

Congenital heart disease assessment with 4D flow MRI

With improvements in surgical and medical management, patients with congenital heart disease (CHD) are often living well into adulthood. MRI provides critical data for diagnosis and monitoring of these patients, yielding information on cardiac anatomy, blood flow, and cardiac function. Though historically these exams have been complex and lengthy, four‐dimensional (4D) flow is emerging as a single fast technique for comprehensive assessment of CHD. The 4D flow consists of a volumetric time‐resolved acquisition that is gated to the cardiac cycle, providing a time‐varying vector field of blood flow as well as registered anatomic images. In this article, we provide an overview of MRI evaluation of congenital heart disease by means of example of three relatively common representative conditions: tetralogy of Fallot, aortic coarctation, and anomalous pulmonary venous drainage. Then 4D flow data acquisition, data correction, and postprocessing techniques are reviewed. We conclude with several examples that highlight the comprehensive nature of the evaluation of congenital heart disease with 4D flow. J. Magn. Reson. Imaging 2015;42:870–886.

Thrombin receptor and RhoA mediate cell proliferation through integrins and cysteine-rich protein 61

A subset of G‐protein coupled receptors (GPCRs), including the thrombin receptor (PARI), elicits mitogenic responses. Thrombin also activates Ras homolog gene family member A (RhoA) and activating protein (AP‐1) ‐mediated gene expression in 1321N1 astrocytoma cells, whereas the nonmitogenic agonist carbachol does not. Transcriptomic analysis was used to explore differential gene induction by these agonists and revealed that the matricellular protein cysteine‐rich 61 (Cyr61/CCN1) is selectively induced by thrombin. The ability of GPCR agonists to induce Cyr61 parallels their ability to activate RhoA;agonist‐stimulated Cyr61 expression is inhibited by C3 toxin. When Cyr61 is down‐regulated using short interfering RNA (siRNA) or short‐hairpin RNA (shRNA), thrombin‐induced DNA synthesis is significantly attenuated. When Cyr61 expression is induced, it appears in the extracellular compartment and on the cell surface. Extracellular Cyr61 interacts with α5, α6, and β1 integrins on these cells, and monoclonal antibodies directed against α5 and β1 integrins inhibit thrombin‐induced DNA synthesis. Functional blockade of Cyr61 with soluble heparin or anti‐Cyr61 antibodies also inhibits thrombin‐induced DNA synthesis. Thus Cyr61 is a highly inducible, secreted extracellular factor through which GPCR and RhoA signaling pathways engage integrins that contribute to GPCR‐mediated proliferation.— Walsh, C. T., Radeff‐Huang, J., Matteo, R., Hsiao, A., Subramaniam, S., Stupack, D., and Brown, J. H. Thrombin receptor and RhoA mediate cell proliferation through integrins and cysteine‐rich protein 61. FASEB J. 22, 4011–4021 (2008)

Improved cardiovascular flow quantification with time-resolved volumetric phase-contrast MRI

BackgroundCardiovascular flow is commonly assessed with two-dimensional, phase-contrast MRI (2-D PC-MRI). However, scan prescription and acquisition over multiple planes is lengthy, often requires direct physician oversight and has inconsistent results. Time-resolved volumetric PC-MRI (4-D flow) may address these limitations.ObjectiveWe assess the degree of agreement and internal consistency between 2-D and 4-D flow quantification in our clinical population.Materials and methodsSoftware enabling flow calculation from 4-D flow was developed in Java. With IRB approval and HIPAA compliance, 18 consecutive patients without shunts were identified who underwent both (1) conventional 2-D PC-MRI of the aorta and main pulmonary artery and (2) 4-D flow imaging. Aortic and pulmonary flow rates were assessed with both techniques.ResultsBoth methods showed general agreement in flow rates (ρ: 0.87–0.90). Systemic and pulmonary arterial flow rates were well-correlated (ρ: 4-D 0.98–0.99, 2-D 0.93), but more closely matched with 4-D (P  <  0.05, Brown-Forsythe). Pulmonary flow rates were lower than systemic rates for 2-D (P  <  0.05, two-sample t-test). In a sub-analysis of patients without pulmonary or aortic regurgitation, 2-D showed improved correlation of flow rates while 4-D phase-contrast remained tightly correlated (ρ: 4-D 0.99–1.00, 2-D 0.99).Conclusion4-D PC-MRI demonstrates greater consistency than conventional 2-D PC-MRI for flow quantification.

Robust 4D flow denoising using divergence-free wavelet transform

To investigate four‐dimensional flow denoising using the divergence‐free wavelet (DFW) transform and compare its performance with existing techniques.

Inlet and outlet valve flow and regurgitant volume may be directly and reliably quantified with accelerated, volumetric phase-contrast MRI

To determine whether it is feasible to use solely an accelerated 4D phase‐contrast magnetic resonance imaging (4D‐PC MRI) acquisition to quantify net and regurgitant flow volume through each of the cardiac valves.

High-throughput biology in the postgenomic era.

HIGH-THROUGHPUT biologicalmethods, namely, methods that per-form thousands of simultaneous mea-surements of biological molecules,have rapidly transformed the land-scape of biomedical research duringthe past decade. Perhaps most centralto this transformation has been the se-quencing of the human genome andsubsequent free release of genomic in-formation, emphasized as a criticalgoal in the Bermuda Statement by par-ticipants of the Human GenomeProject (1). With this massive under-taking largely completed, investiga-tors are faced with new tools andunique challenges in this postgenomicera. The large volume of informationgenerated by the Human GenomeProject has facilitated the developmentof many novel platforms for profilingeach stage in the flow of biologicalinformation: from DNA to RNA toprotein to the myriad of protein inter-actions, inspiring advancement of theburgeoning new areas of genomics,transcriptomics, proteomics, and in-teractomics, respectively.Collectively, these core aspects ofmodern high-throughput biology eachaim to provide a cross-sectional snap-shot of fundamental biology to simul-taneously assess the direct or down-stream influence of thousands ofgenes. Ultimately, this may allow us tothen identify and characterize the en-tire space of biomolecules that consti-tute the composite catalogue of possi-ble therapeutic targets and their rolesin disease, and to thereby affect dis-ease at a molecular level through im-proved rational design of new classesof micro- and nanoscale moleculartherapeutic agents and bioactive med-ical devices. Improved understandingof individual targets promises to beuseful in the assessment of risk, diag-nosis, prognosis, and therapy of hu-man disease, lending to the possibili-ties of personalized medicine.As these high-throughput biologi-cal tools have the potential to intro-duce significant changes that could af-fect the practice of clinical medicine, itis critical that interventional radiolo-gists understand them so they can crit-ically evaluate and integrate them di-rectly into their own research andclinical efforts.Herein we review the implicationsof high-throughput biology in thepostgenomic era for biomedical re-search and clinical practice. In the firstsection, we discuss the basic principlesbehind high-throughput tools. Weprincipally focus on array-based high-throughput biological methods, a keyhigh-throughput biological tool, anddescribe how they are being used touncover different aspects of biology.In the second half, we discuss inter-pretation of high-throughput data andthe challenges high-throughput bio-logical techniques present for dataanalysis. These discussions provide anunderstanding of the high-throughputtechnologies currently being appliedin basic research, the biomedical ques-tions they can be used to address, anda foundation for the interpretation ofnovel results.