For personalized genomic medicine to be a reality, two things must happen: First, we need to directly establish the role of genetic variation in disease incidence and progression, rather than studying genetic associations and molecular mechanisms in isolation from each other. Second, we must investigate the networks of biological molecules responsible for complex diseases like cardiovascular disease as emergent molecular phenotypes, while at the same time using targeted strategies to establish causal relationships. Together, these innovations can lead to an understanding of how genetic variability combines with environmental stimuli to influence disease susceptibility. The goal of this multi-PI grant is to advance the field toward genomic medicine for common forms of heart failure. It is well established that global changes in gene expression accompany the transition through cardiac hypertrophy and on to failure in animals and humans, causing cellular remodeling and deterioration of cardiac function. We reason that cues from the primary DNA sequence, modification of DNA (i.e. methylation) and chromatin-associated proteins (e.g. CTCF) and noncoding RNA (e.g. C5) combine to specify genomic structure and thereby gene expression. In this model, genomic conformation determines the range of phenotypic possibilities in an individual subjected to pathological stimuli by favoring some gene/protein expression profiles and disfavoring others. Our overall hypothesis is that epigenomic features, including DNA methylation and chromatin accessibility, set the baseline plasticity of chromatin structure and are influenced by genetics and environmental stimuli, such that some individuals are more susceptible than others to heart failure. We reason that global regulators of chromatin accessibility, including the novel epigenetic modifier C5 and the structural protein CTCF, play central roles in disease associated gene reprogramming. In the first aim, we will identify how transcription is regulated by the local chromatin landscape at genes, by dissecting the genetic contribution to DNA methylation (BS-seq) and chromatin accessibility (FAIRE- seq) in the normal and stressed heart. In the second aim, we will determine how intermediate chromatin domains are regulated in heart failure by exploring the role of a cardiac-specific lncRNA C5 to target deposition of heterochromatic histone modifications. In the third aim, we will identify the mechanisms of global chromatin conformation in cardiac health and disease by determining the involvement of the master genome architectural protein CTCF in cardiac phenotype. The long-term goals of these studies are to determine the mechanisms for how genetic variation controls differential disease susceptibility and to investigate epigenomic features as both biomarkers for cardiac pathology and causal components of cellular dysfunction.
Cardiovascular disease is a scourge on human health for which transformative studies of its mechanisms are needed. This proposal will test the hypothesis that genome-wide changes in DNA methylation and chromatin accessibility together control heart failure susceptibility-furthermore, we will mechanistically reveal the roles of the lncRNA C5 and the master genome regulator CTCF in cardiac function. These investigations have the potential to establish new approaches for treating the diverse syndrome of heart failure in humans.
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