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  • Epistasis regulates genetic control of cardiac hypertrophy. Research square Wang, Q., Tang, T. M., Youlton, N., Weldy, C. S., Kenney, A. M., Ronen, O., Hughes, J. W., Chin, E. T., Sutton, S. C., Agarwal, A., Li, X., Behr, M., Kumbier, K., Moravec, C. S., Tang, W. H., Margulies, K. B., Cappola, T. P., Butte, A. J., Arnaout, R., Brown, J. B., Priest, J. R., Parikh, V. N., Yu, B., Ashley, E. A. 2023

    Abstract

    The combinatorial effect of genetic variants is often assumed to be additive. Although genetic variation can clearly interact non-additively, methods to uncover epistatic relationships remain in their infancy. We develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy. We derive deep learning-based estimates of left ventricular mass from the cardiac MRI scans of 29,661 individuals enrolled in the UK Biobank. We report epistatic genetic variation including variants close to CCDC141, IGF1R, TTN, and TNKS. Several loci not prioritized by univariate genome-wide association analysis are identified. Functional genomic and integrative enrichment analyses reveal a complex gene regulatory network in which genes mapped from these loci share biological processes and myogenic regulatory factors. Through a network analysis of transcriptomic data from 313 explanted human hearts, we show that these interactions are preserved at the level of the cardiac transcriptome. We assess causality of epistatic effects via RNA silencing of gene-gene interactions in human induced pluripotent stem cell-derived cardiomyocytes. Finally, single-cell morphology analysis using a novel high-throughput microfluidic system shows that cardiomyocyte hypertrophy is non-additively modifiable by specific pairwise interactions between CCDC141 and both TTN and IGF1R. Our results expand the scope of genetic regulation of cardiac structure to epistasis.

    View details for DOI 10.21203/rs.3.rs-3509208/v1

    View details for PubMedID 38045390

    View details for PubMedCentralID PMC10690313

  • Epistasis regulates genetic control of cardiac hypertrophy. medRxiv : the preprint server for health sciences Wang, Q., Tang, T. M., Youlton, N., Weldy, C. S., Kenney, A. M., Ronen, O., Hughes, J. W., Chin, E. T., Sutton, S. C., Agarwal, A., Li, X., Behr, M., Kumbier, K., Moravec, C. S., Tang, W. H., Margulies, K. B., Cappola, T. P., Butte, A. J., Arnaout, R., Brown, J. B., Priest, J. R., Parikh, V. N., Yu, B., Ashley, E. A. 2023

    Abstract

    The combinatorial effect of genetic variants is often assumed to be additive. Although genetic variation can clearly interact non-additively, methods to uncover epistatic relationships remain in their infancy. We develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy. We derive deep learning-based estimates of left ventricular mass from the cardiac MRI scans of 29,661 individuals enrolled in the UK Biobank. We report epistatic genetic variation including variants close to CCDC141, IGF1R, TTN, and TNKS. Several loci not prioritized by univariate genome-wide association analysis are identified. Functional genomic and integrative enrichment analyses reveal a complex gene regulatory network in which genes mapped from these loci share biological processes and myogenic regulatory factors. Through a network analysis of transcriptomic data from 313 explanted human hearts, we show that these interactions are preserved at the level of the cardiac transcriptome. We assess causality of epistatic effects via RNA silencing of gene-gene interactions in human induced pluripotent stem cell-derived cardiomyocytes. Finally, single-cell morphology analysis using a novel high-throughput microfluidic system shows that cardiomyocyte hypertrophy is non-additively modifiable by specific pairwise interactions between CCDC141 and both TTN and IGF1R. Our results expand the scope of genetic regulation of cardiac structure to epistasis.

    View details for DOI 10.1101/2023.11.06.23297858

    View details for PubMedID 37987017

    View details for PubMedCentralID PMC10659487

  • Improved Cardiac Performance and Decreased Arrhythmia in Hypertrophic Cardiomyopathy With Non-β-Blocking R-Enantiomer Carvedilol. Circulation Seo, K., Yamamoto, Y., Kirillova, A., Kawana, M., Yadav, S., Huang, Y., Wang, Q., Lane, K. V., Pruitt, B. L., Perez, M. V., Bernstein, D., Wu, J. C., Wheeler, M. T., Parikh, V. N., Ashley, E. A. 2023

    Abstract

    Hypercontractility and arrhythmia are key pathophysiologic features of hypertrophic cardiomyopathy (HCM), the most common inherited heart disease. β-Adrenergic receptor antagonists (β-blockers) are the first-line therapy for HCM. However, β-blockers commonly selected for this disease are often poorly tolerated in patients, where heart-rate reduction and noncardiac effects can lead to reduced cardiac output and fatigue. Mavacamten, myosin ATPase inhibitor recently approved by the US Food and Drug Administration, has demonstrated the ability to ameliorate hypercontractility without lowering heart rate, but its benefits are so far limited to patients with left ventricular (LV) outflow tract obstruction, and its effect on arrhythmia is unknown.We screened 21 β-blockers for their impact on myocyte contractility and evaluated the antiarrhythmic properties of the most promising drug in a ventricular myocyte arrhythmia model. We then examined its in vivo effect on LV function by hemodynamic pressure-volume loop analysis. The efficacy of the drug was tested in vitro and in vivo compared with current therapeutic options (metoprolol, verapamil, and mavacamten) for HCM in an established mouse model of HCM (Myh6R403Q/+ [myosin heavy chain 6]) and iPSC cardiomyocytes derived from patients with HCM (MYH7R403Q/+) [myosin heavy chain 7]).We identified that carvedilol, a β-blocker not commonly used in HCM, suppresses contractile function and arrhythmia by inhibiting RyR2 (ryanodine receptor type 2). Unlike metoprolol (a β1-blocker), carvedilol markedly reduced LV contractility through RyR2 inhibition, while maintaining stroke volume through α1-adrenergic receptor inhibition in vivo. Clinically available carvedilol is a racemic mixture, and the R-enantiomer, devoid of β-blocking effect, retains the ability to inhibit both α1-receptor and RyR2, thereby suppressing contractile function and arrhythmias without lowering heart rate and cardiac output. In Myh6R403Q/+ mice, R-carvedilol normalized hyperdynamic contraction, suppressed arrhythmia, and increased cardiac output better than metoprolol, verapamil, and mavacamten. The ability of R-carvedilol to suppress contractile function was well retained in MYH7R403Q/+ induced pluripotent stem cell cardiomyocytes.R-enantiomer carvedilol attenuates hyperdynamic contraction, suppresses arrhythmia, and at the same time, improves cardiac output without lowering heart rate by dual blockade of α1-adrenergic receptor and RyR2 in mouse and human models of HCM. This combination of therapeutic effects is unique among current therapeutic options for HCM and may particularly benefit patients without LV outflow tract obstruction.

    View details for DOI 10.1161/CIRCULATIONAHA.123.065017

    View details for PubMedID 37850394

  • Leveraging microfluidic dielectrophoresis to distinguish compositional variations of lipopolysaccharide in E. coli FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY Wang, Q., Kim, H., Halvorsen, T. M., Chen, S., Hayes, C. S., Buie, C. R. 2023; 11: 991784

    Abstract

    Lipopolysaccharide (LPS) is the unique feature that composes the outer leaflet of the Gram-negative bacterial cell envelope. Variations in LPS structures affect a number of physiological processes, including outer membrane permeability, antimicrobial resistance, recognition by the host immune system, biofilm formation, and interbacterial competition. Rapid characterization of LPS properties is crucial for studying the relationship between these LPS structural changes and bacterial physiology. However, current assessments of LPS structures require LPS extraction and purification followed by cumbersome proteomic analysis. This paper demonstrates one of the first high-throughput and non-invasive strategies to directly distinguish Escherichia coli with different LPS structures. Using a combination of three-dimensional insulator-based dielectrophoresis (3DiDEP) and cell tracking in a linear electrokinetics assay, we elucidate the effect of structural changes in E. coli LPS oligosaccharides on electrokinetic mobility and polarizability. We show that our platform is sufficiently sensitive to detect LPS structural variations at the molecular level. To correlate electrokinetic properties of LPS with the outer membrane permeability, we further examined effects of LPS structural variations on bacterial susceptibility to colistin, an antibiotic known to disrupt the outer membrane by targeting LPS. Our results suggest that microfluidic electrokinetic platforms employing 3DiDEP can be a useful tool for isolating and selecting bacteria based on their LPS glycoforms. Future iterations of these platforms could be leveraged for rapid profiling of pathogens based on their surface LPS structural identity.

    View details for DOI 10.3389/fbioe.2023.991784

    View details for Web of Science ID 000942533100001

    View details for PubMedID 36873367

    View details for PubMedCentralID PMC9979706

  • Microfluidic dielectrophoresis illuminates the relationship between microbial cell envelope polarizability and electrochemical activity. Science advances Wang, Q., Jones, A. D., Gralnick, J. A., Lin, L., Buie, C. R. 2019; 5 (1): eaat5664

    Abstract

    Electrons can be transported from microbes to external insoluble electron acceptors (e.g., metal oxides or electrodes in an electrochemical cell). This process is known as extracellular electron transfer (EET) and has received considerable attention due to its applications in environmental remediation and energy conversion. However, the paucity of rapid and noninvasive phenotyping techniques hinders a detailed understanding of microbial EET mechanisms. Most EET phenotyping techniques assess microorganisms based on their metabolism and growth in various conditions and/or performance in electrochemical systems, which requires large sample volumes and cumbersome experimentation. Here, we use microfluidic dielectrophoresis to show a strong correlation between bacterial EET and surface polarizability. We analyzed surface polarizabilities for wild-type strains and cytochrome-deletion mutants of two model EET microbes, Geobacter sulfurreducens and Shewanella oneidensis, and for Escherichia coli strains heterologously expressing S. oneidensis EET pathways in various growth conditions. Dielectrophoretic phenotyping is achieved with small cell culture volumes (~100 μl) in a short amount of time (1 to 2 min per strain). Our work demonstrates that cell polarizability is diminished in response to deletions of crucial outer-membrane cytochromes and enhanced due to additions of EET pathways. Results of this work hold exciting promise for rapid screening of direct EET or other cell envelope phenotypes using cell polarizability as a proxy, especially for microbes difficult to cultivate in laboratory conditions.

    View details for DOI 10.1126/sciadv.aat5664

    View details for PubMedID 30746438

    View details for PubMedCentralID PMC6357865

  • Nonlinear electrokinetic effects in insulator-based dielectrophoretic systems. Electrophoresis Wang, Q., Dingari, N. N., Buie, C. R. 2017; 38 (20): 2576-2586

    Abstract

    Insulator-based dielectrophoresis (iDEP) has emerged as a powerful tool for multiple biomicrofluidic operations, such as cell separation and concentration. The key feature for iDEP systems is the alteration of insulating microchannel geometries to create strong electric field gradients. Under AC electric fields, this strong electric field gradient can affect fluid flow by (at least) two nonlinear electrokinetic phenomena; (a) electrothermal flow due to Joule heating and (b) induced charge electroosmosis (ICEO) near the microchannel constrictions of small (but finite) permittivity and conductivity. This paper presents an experimental and theoretical study on the interplay of electrothermal and ICEO flows near microchannel constrictions with various geometries and fluid ionic strengths, which are crucial design factors for iDEP systems. Temperature rise and fluid velocities in 2D Gaussian-shaped constrictions were studied experimentally with supporting analytical estimations and numerical simulations. Additionally, we show qualitatively distinct recirculating flow patterns in 2D and 3D microchannel constrictions used for iDEP systems. Approximate analytical expressions for electrothermal and ICEO velocity scales are provided as a function of constriction geometry, bulk electrolyte concentration, and the applied electric field. Insights from this study will be useful in designing microfluidic systems for electrokinetic particle manipulation.

    View details for DOI 10.1002/elps.201700144

    View details for PubMedID 28763135