The heart consists of a multitude of diverse cardiac cell types, including but not limited to cardiomyocytes, cardiac fibroblasts, epicardial cells, endothelial/endocardial cells and smooth muscle cells, which coordinate to sustain cardiac function and circulation throughout the body. Thus, regulated maintenance of these cell types is crucial for optimal heart performance and disrupting the function of specific cell lineages can result in distinct heart diseases including heart failure, which is a major leading cause of morbidity and mortality worldwide. However, what are the specific cell lineages affected during heart failure and how do gene regulatory networks control genetic programs that direct their pathologic outcomes are key biomedical questions that remain to be resolved. To address these issues, we have created an interdisciplinary team that includes physician-scientists who will collect patient heart tissue samples to investigate molecular mechanisms involved in the pathogenesis of heart failure; genomic and epigenomic experts who will employ cutting-edge single-cell sequencing and chromatin analysis technologies to examine cell-type specific chromatin accessibility-interactions and corresponding gene expression; and stem cell biologists who will utilize human pluripotent stem cell cardiac models and state-of-the-art genome-editing strategies to perform functional confirmation studies. Through these integrative efforts and analyses, we plan to examine the hypothesis that cis-regulatory elements and their enhancer-promoter interactions dynamically function and coordinate in a cell- type specific manner to direct lineage-specific gene expression during cardiac tissue homeostasis, and altering these highly-regulated cell-type specific cis-regulatory elements and corresponding gene regulatory networks can lead to heart failure. Specifically, we propose to 1) identify cis-regulatory elements and cell-types that are affected by heart failure-associated non-coding genetic variants; 2) investigate how gene regulatory networks controlling specific cardiovascular cell-types are altered during heart failure; and 3) examine how perturbations of cell-type specific cis-regulatory elements and gene regulatory networks during heart failure impact cell function and gene expression.

Public Health Relevance

The following proposal seeks to illuminate the underlying cell-type specific molecular mechanisms regulating the pathogenesis of heart failure. Results from these studies will identify the affected cell-types during heart failure, reveal the molecular mechanisms directing their pathologic outcomes and provide insight into developing precise cardiac diagnostics and therapies that are tailored to affected cell-types, thus optimizing therapeutic efficacy for treating heart failure.

National Institute of Health (NIH)
National Heart, Lung, and Blood Institute (NHLBI)
Research Project (R01)
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Cardiac Contractility, Hypertrophy, and Failure Study Section (CCHF)
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Shi, Yang
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University of California, San Diego
Internal Medicine/Medicine
Schools of Medicine
La Jolla
United States
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