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Biology subjects

Holmes, J. W.

Publications and source records attributed to Holmes, J. W..

7 recordsLinked to original sources

Contributions of mechanical loading and hormonal changes to eccentric hypertrophy during volume overload: a Bayesian analysis using logic-based network models.

Primary mitral regurgitation (MR) is a pathology that alters mechanical loading on the left ventricle, triggers an array of compensatory neurohormonal responses, and induces a distinctive ventricular remodeling response known as eccentric hypertrophy. Drug therapies may alleviate symptoms, but only mitral valve repair or replacement can provide significant recovery of cardiac function and dimensions. Questions remain about the optimal timing of surgery, with 20% of patients developing systolic dysfunction post-operatively despite being treated according to the current guidelines. Thus, better understanding of the hypertrophic process in the setting of ventricular volume overload (VO) is needed to improve and better personalize the management of MR. To address this knowledge gap, we employ a Bayesian approach to combine data from 70 studies on experimental volume overload in dogs and rats and use it to calibrate a logic-based network model of hypertrophic signaling in myocytes. The calibrated model predicts that growth in experimental VO is mostly driven by the neurohormonal response, with an initial increase in myocardial tissue stretch being compensated by subsequent remodeling fairly early in the time course of VO. This observation contrasts with a common perception that volume-overload hypertrophy is driven primarily by increased myocyte strain. The model reproduces many aspects of 43 studies not used in its calibration, including infusion of individual hypertrophic agonists alone or in combination with various drugs commonly employed to treat heart failure, as well as administration of some of those drugs in the setting of experimental volume overload. We believe this represents a promising approach to using the known structure of an intracellular signaling network to integrate information from multiple studies into quantitative predictions of the range of expected responses to potential interventions in the complex setting of cardiac hypertrophy driven by a combination of hormonal and mechanical factors. Author SummaryMitral valve regurgitation is a common heart disease in which a malfunctioning valve allows part of the blood pumped by the heart to flow in the wrong direction. This condition overloads the heart by making it pump more blood volume than normal; the heart temporarily adapts by growing in mass and volume, but if untreated the condition can ultimately lead to heart failure and death. The most effective treatment is to surgically repair the valve; however, in many patients heart function deteriorates even after a successful surgery. Many researchers have studied this condition by experimentally overloading the hearts of dogs and rats, producing large amounts of data on the resulting geometric, mechanical, and biologic changes. Yet it has been difficult to translate those studies into effective selection and timing of treatment in all patients. In this work we integrate experimental data reported from 70 research articles on experimental volume overload through a simple model of heart mechanics and a more complex model of the molecular signaling pathways inside heart cells. We use a statistical approach to calibrate the computational model, so that it can predict not only average responses but also the degree of expected uncertainty for each prediction. We then use the model to explore how the heart responds to different combinations of drugs and hormones, and potential treatments during overload.

bioengineering↗

Automated Spatially Targeted Optical Micro Proteomics (AutoSTOMP) 2.0 identifies proteins enriched within inflammatory lesions in tissue sections and human clinical biopsies.

Tissue microenvironment properties like blood flow, extracellular matrix or proximity to immune infiltrate are important regulators of cell biology. However, methods to study regional protein expression in context of the native tissue environment are limited. To address this need we have developed a novel approach to visualize, purify and measure proteins in situ using Automated Spatially Targeted Optical Micro Proteomics (AutoSTOMP) 2.0. We previously implemented AutoSTOMP to identify proteins localized to the vacuoles of obligate intracellular microbes at the 1-2 m scale within infected host cells1. Here we report custom codes in SikuliX to specify regions of heterogeneity in a tissue section and then biotin tag and identify proteins belonging to specific cell types or structures within those regions. To enrich biotinylated targets from fixed tissue samples we developed a biochemical protocol compatible with LC-MS. These tools were applied to a) identify inflammatory proteins expressed by CD68+ macrophages in rat cardiac infarcts and b) characterize inflammatory proteins enriched in IgG4+ lesions in esophageal tissue. These data indicate that AutoSTOMP is a flexible approach to determine regional protein expression in situ on a range of primary tissues and clinical biopsies where current tools are limited.

immunology↗

A Rapid Electromechanical Model To Predict Reverse Remodeling Following Cardiac Resynchronization Therapy

Cardiac resynchronization therapy (CRT) is an ef-fective therapy for patients who suffer from heart failure and ventricular dyssynchrony such as left bundle branch block (LBBB). When it works, it reverses adverse left ventricular (LV) remodeling and the progression of heart failure. How-ever, CRT response rate is currently as low as 50-65%. In theory, CRT outcome could be improved by allowing clinicians to tailor the therapy through patient-specific lead locations, timing, and/or pacing protocol. However, this also presents a dilemma: there are far too many possible strategies to test during the implantation surgery. Computational models could address this dilemma by predicting remodeling outcomes for each patient before the surgery takes place. Therefore, the goal of this study was to develop a rapid computational model to predict reverse LV remodeling following CRT. We adapted our recently developed computational model of LV remodeling to simulate the mechanics of ventricular dyssynchrony and added a rapid electrical model to predict electrical activation timing. The model was calibrated to quantitatively match changes in hemodynamics and global and local LV wall mass from a canine study of LBBB and CRT. The calibrated model was used to investigate the influence of LV lead location and ischemia on CRT remodeling outcome. Our model results suggest that remodeling outcome varies with both lead location and ischemia location, and does not always correlate with short-term improvement in QRS duration. The results and time frame required to customize and run this model suggest promise for this approach in a clinical setting.

bioengineering↗

Multiscale model of heart growth during pregnancy: Integrating mechanical and hormonal signaling

Pregnancy stands at the interface of mechanics and biology. The growing fetus continuously loads the maternal organs as circulating hormone levels surge, leading to significant changes in mechanical and hormonal cues during pregnancy. In response, maternal soft tissues undergo remarkable growth and remodeling to support the mother and baby for a healthy pregnancy. We focus on the maternal left ventricle, which increases its cardiac output and mass during pregnancy. This study develops a multiscale cardiac growth model for pregnancy to understand how mechanical and hormonal cues interact to drive this growth process. We coupled a cell signaling network model that predicts cell-level hypertrophy in response to hormones and stretch to a compartmental model of the rat heart and circulation that predicts organ-level growth in response to hemodynamic changes. We calibrated this multiscale model to data from experimental volume overload (VO) and hormonal infusions of angiotensin 2 (AngII), estrogen (E2), and progesterone (P4). We then validated the models ability to capture interactions between inputs by comparing model predictions against published observations for the combinations of VO+E2 and AngII+E2. Finally, we simulated pregnancy-induced changes in hormones and hemodynamics to predict heart growth during pregnancy. Our model produced growth consistent with experimental data. Overall, our analysis suggests that the rise in P4 during the first half of gestation is an important contributor to heart growth during pregnancy. We conclude with suggestions for future experimental studies that will provide a better understanding of how hormonal and mechanical cues interact to drive pregnancy-induced heart growth.

bioengineering↗

The Connexin 43 Carboxyl Terminal Mimetic Peptide alphaCT1 Prompts Differentiation of a Collagen Scar Matrix Resembling Unwounded Skin

Phase II clinical trials have reported that acute treatment of surgical skin wounds with the therapeutic peptide αCT1 improves cutaneous scar appearance by 47% 9-months post-surgery – though mode-of-action remains unknown. Scar matrix structure in biopsies 2 to 6 weeks post-wounding treated topically with αCT1 or control treatments from human subjects, Sprague-Dawley rats, and IAF hairless guinea pigs were compared. The sole effect on scar structure in humans was that αCT1-treated scars had less alignment of collagen fibers relative to control wounds, a state that resembles unwounded skin. This more random alignment was recapitulated in both animal models, together with transient increases in collagen density, although the guinea pig was found to more closely replicate the pattern of response to αCT1 in human scars, compared to rat. Fibroblasts treated with αCT1 in vitro showed decreased directionality and an agent-based computational model parameterized with fibroblast motility data predicted collagen alignments in simulated scars consistent with that observed experimentally in human and the animal models. In conclusion, αCT1 prompts decreased directionality of fibroblast movement and the generation of a 3D collagen matrix post-wounding that is similar to unwounded skin – changes that correlate with long-term improvement in scar appearance.Competing Interest StatementGSG is CEO and President of FirstString Research Inc. CLG is Senior Director of Research and Development at FirstString Research Inc. RGG is a non-remunerated member of the Scientific Advisory Board of FirstString Research, which licensed α carboxyl terminus 1 peptide. GSG, RGG, LJJ, and CLG have ownership interests in FirstString Research Inc. The remaining authors have no disclosures to report.View Full Text

cell biology↗

Mechano-Chemo Signaling Interactions Modulate Matrix Production by Cardiac Fibroblasts

Extracellular matrix remodeling after myocardial infarction occurs in a dynamic environment in which local mechanical stresses and biochemical signaling species stimulate the accumulation of collagen-rich scar tissue. It is well-known that cardiac fibroblasts regulate post-infarction matrix turnover by secreting matrix proteins, proteases, and protease inhibitors in response to both biochemical stimuli and mechanical stretch, but how these stimuli act together to dictate cellular responses is still unclear. We developed a screen of cardiac fibroblast-secreted proteins in response to combinations of biochemical agonists and cyclic uniaxial stretch in order to elucidate the relationships between stretch, biochemical signaling, and cardiac matrix turnover. We found that stretch significantly synergized with biochemical agonists to inhibit the secretion of matrix metalloproteinases, with stretch either amplifying protease suppression by individual agonists or antagonizing agonist-driven upregulation of protease expression. Stretch also modulated fibroblast sensitivity towards biochemical agonists by either sensitizing cells towards agonists that suppress protease secretion or de-sensitizing cells towards agonists that upregulate protease secretion. These findings suggest that the mechanical environment can significantly alter fibrosis-related signaling in cardiac fibroblasts, suggesting caution when extrapolating in vitro data to predict effects of fibrosis-related cytokines in situations like myocardial infarction where mechanical stretch occurs.

bioengineering↗

Computational Model Predicts Paracrine and Intracellular Drivers of Fibroblast Phenotype After Myocardial Infarction

The fibroblast is a key mediator of wound healing in the heart and other organs, yet how it integrates multiple time-dependent paracrine signals to control extracellular matrix synthesis has been difficult to study in vivo. Here, we extended a computational model to simulate the dynamics of fibroblast signaling and fibrosis after myocardial infarction in response to time-dependent data for nine paracrine stimuli. This computational model was validated against dynamic collagen expression and collagen area fraction data from post-infarction rat hearts. The model predicted that while many features of the fibroblast phenotype at inflammatory or maturation phases of healing could be recapitulated by single static paracrine stimuli (interleukin-1 and angiotensin-II, respectively), mimicking of the proliferative phase required paired stimuli (e.g. TGF{beta} and angiotensin-II). Virtual overexpression screens with static cytokine pairs and after myocardial infarction predicted phase-specific regulators of collagen expression. Several regulators increased (Smad3) or decreased (Smad7, protein kinase G) collagen expression specifically in the proliferative phase. NADPH oxidase overexpression sustained collagen expression from proliferative to maturation phases, driven by TGF{beta} and endothelin positive feedback loops. Interleukin-1 overexpression suppressed collagen via NF{kappa}B and BAMBI (BMP and activin membrane-bound inhibitor) incoherent feedforward loops, but it then later sustained collagen expression due to the TGF{beta} positive feedback loop. These model-based predictions reveal network mechanisms by which the dynamics of paracrine stimuli and interacting signaling pathways drive the progression of fibroblast phenotypes and fibrosis after myocardial infarction.

systems biology↗