Biology subjects

Richardson, W. J.

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

6 recordsLinked to original sources

bioRxiv2025

Heart Scar-In-A-Dish: Tissue Culture Platform to Study Myocardial Infarct Healing In Vitro

Myocardial Infarction (MI) is a major contributor to morbidity and mortality, wherein blood flow is blocked to a portion of the left ventricle and leads to myocardial necrosis and scar formation. Cardiac remodeling in response to MI is a major determinant of patient prognosis, so many therapies are under development to improve infarct healing. Part of this development involves in vitro therapy screening which can be accelerated by engineered heart tissues (EHTs). Unfortunately, EHTs often over-simplify the infarcted tissue microarchitecture by neglecting spatial variation found in infarcted ventricles. MI results in a spatially heterogeneous environment with an infarct zone composed mostly of extracellular matrix (ECM) and cardiac fibroblasts, contrasted with a remote (non-infarct) zone composed mostly of cardiomyocytes, and a border zone transitioning in between. The heterogeneous structure is accompanied by heterogeneous mechanics where the passive infarct zone is cyclically stretched under tension as the remote zone cyclically contracts with every heartbeat. We present an in vitro 3-dimensional tissue culture platform focused on mimicking the heterogeneous mechanical environment of post-infarct myocardium. Herein, EHTs were subjected to a cryowound injury to induce localized cell death in a central portion of beating tissues composed of neonatal rat cardiomyocytes and cardiac fibroblasts. After injury, the remote zone continued to contract (i.e., negative strains) while the wounded zone was cyclically stretched (i.e., positive tensile strains) with intermediate strains in the border zone. We also observed increased tissue stiffnesses in the wounded zone and border zone following injury, while the remote zone did not show the same stiffening. Collectively, this work establishes a novel in vitro platform for characterizing myocardial wound remodeling with both spatial and temporal resolution, contributing to a deeper understanding of MI and offering insights for potential therapeutic approaches.

bioengineering↗

bioRxiv2025

Sensitivity Analysis to Isolate the Effects of Proteases and Protease Inhibitors on Extracellular Matrix Turnover

Matrix metalloproteinases (MMPs) are a family of proteases that drive degradation of extracellular matrix (ECM) across many tissues. MMP activity is antagonized by tissue inhibitors of metalloproteinases (TIMPs), resulting in a complex multivariate system with many MMP isoforms and TIMP isoforms interacting across a network of biochemical reactions - each with their own distinct kinetic rates. This system complexity makes it very difficult to identify which specific molecules are most responsible for driving ECM turnover in vivo and therefore the most promising therapeutic targets. To help elucidate the specific roles of various MMP and TIMP isoforms, we present a computational systems biology model of collagen turnover capturing all possible interactions between type I collagen, four different MMP isoforms (MMP-1, -2, -8, and -9), and three different TIMP isoforms (TIMP-1, -2, and -4). We used dye-quenched fluorescent collagen to monitor the degradation of collagen in the presence of various MMP+TIMP cocktails, and we then used these experimental data to fit hypothetical reaction system topologies in order to investigate their respective accuracies. We determined kinetic rate constants for this system and used post-myocardial infarct time courses of collagen, MMP, and TIMP levels to perform a parameter sensitivity analysis across the model reaction rates and predict which molecules and interactions are the important regulators of ECM in the infarcted heart. Notably, the model suggested that MMP degradation and inactivation terms were more important for driving collagen levels than TIMP interaction terms. In sum, this work highlights the need for systems-level analyses to distinguish the roles of various biomolecules operating with a complex system, prioritizes therapeutic targets for post-infarct cardiac remodeling, and presents a computational framework that can be applied to many other collagen-rich tissues.

systems biology↗

bioRxiv2023

Computational Screen for Sex-Specific Drug Effects in a Cardiac Fibroblast Network Model

Heart disease is the leading cause of death in both men and women. Cardiac fibrosis is the uncontrolled accumulation of extracellular matrix proteins which can exacerbate the progression of heart failure, and there are currently no drugs approved specifically to target matrix accumulation in the heart. Computational signaling network models (SNMs) can be used to facilitate discovery of novel drug targets. However, the vast majority of SNMs are not sex-specific and/or are developed and validated using data skewed towards male in vitro and in vivo samples. Biological sex is an important consideration in cardiovascular health and drug development. In this study, we integrate a previously constructed cardiac fibroblast SNM with estrogen signaling pathways to create sex-specific SNMs. The sex-specific SNMs maintained previously high validation when compared to in vitro experimental studies in the literature. A sex-specific perturbation analysis and drug screen uncovered several potential pathways that warrant further study in the pursuit of sex-specific treatment recommendations for cardiac fibrosis. Author SummaryHeart failure is a leading cause of death for both men and women, but we still do not have adequate therapies to prevent or reverse this disease. One factor that contributes to heart failure is scarring of cardiac tissue, also known as fibrosis. Computer models can help find new heart failure drugs by simulating hundreds of biological reactions that regulate fibrosis at the molecular level. Unfortunately, the differences in male and female patients are not usually considered for these drug discovery simulations, which can result in drugs that work well for some individuals but not for other individuals. In our study, we added sex-specific biological reactions to a computer model in order to identify drugs that could treat fibrosis differently in male and female patients. Our simulations also predicted why premenopausal women may generally develop less fibrosis than men, while post-menopausal women may develop similar levels of fibrosis as men.

systems biology↗

bioRxiv2021

Network Modeling Predicts Personalized Gene Expression and Drug Responses in Valve Myofibroblasts Cultured with Patient Sera

Aortic valve stenosis (AVS) patients experience pathogenic valve leaflet stiffening due to excessive extracellular matrix (ECM) remodeling. Numerous microenvironmental cues influence pathogenic expression of ECM remodeling genes in tissue-resident valvular myofibroblasts, and the regulation of complex myofibroblast signaling networks depends on patient-specific extracellular factors. Here, we combined a manually curated myofibroblast signaling network with a data-driven transcription factor network to predict patient-specific myofibroblast gene expression signatures and drug responses. Using transcriptomic data from myofibroblasts cultured with AVS patient sera, we produced a large-scale, logic-gated differential equation model in which 11 biochemical and biomechanical signals are transduced via a network of 334 signaling and transcription reactions to accurately predict the expression of 27 fibrosis-related genes. Correlations were found between personalized model-predicted gene expression and AVS patient echocardiography data, suggesting links between fibrosis-related signaling and patient-specific AVS severity. Further, global network perturbation analyses revealed signaling molecules with the most influence over network-wide activity including endothelin 1 (ET1), interleukin 6 (IL6), and transforming growth factor {beta} (TGF{beta}) along with downstream mediators c-Jun N-terminal kinase (JNK), signal transducer and activator of transcription (STAT), and reactive oxygen species (ROS). Lastly, we performed virtual drug screening to identify patient-specific drug responses, which were experimentally validated via fibrotic gene expression measurements in VICs cultured with AVS patient sera and treated with or without bosentan - a clinically approved ET1 receptor inhibitor. In sum, our work advances the ability of computational approaches to provide a mechanistic basis for clinical decisions including patient stratification and personalized drug screening.

systems biology↗

bioRxiv2020

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↗

bioRxiv2020

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↗