Genomic structural dynamics in fibroblasts during heart failure

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ABSTRACT Heart failure is a debilitating syndrome that results in depletion of oxygen and nutrients in critical organs for survival and is associated with left ventricular dysfunction and deposition of scar tissue by fibroblasts. Although genetic mutations partially explain the etiology of phenotypic dysfunction in the heart, disease gene expression programs and organ-level pathology are routinely observed in patients with no family history of heart failure. At a global level, chromatin is organized into: higher order regions that interact with themselves more than with others, so-called topologically associating domains (TADs); active and inactive compartments that tend to contain regions of higher or lower transcription, respectively; and chromosome territories. Cardiac chromatin structure is deranged with heart failure, as measured by high-throughput chromatin conformation capture (Hi-C). In addition, chromatin architecture plays a role in conferring cell-type specific transcriptomes and 3D modeling of Hi-C contacts into populations of structures reveals differential rules for cell-type specific gene positioning and genome compartmentalization. A major gap in our understanding is the relationship between local and long range chromatin interactions in conferring disease specific global nuclear structure. To this end, we propose defining 3D chromatin architectural dynamics with fibroblast disease, to reveal how disease gene expression paradigms are driven with pathological stimulus. In Aim 1 we will use high-throughput sequencing and computational modeling to generate integrated 3D models of healthy and activated fibroblast genomes to understand spatial relationships between genomic regulatory regions in disease. Because modeling generates a population of structures, we can model how structural changes in a population of nuclei contribute to organ level response, and how classes of genes undergo coordinated actions in 3D. In Aim 2 we will advance these genomic models by validating findings with orthogonal techniques. We will perform 3D FISH on candidate genes from our models to confirm these spatial changes in vivo with pressure overload mediated heart failure. In isolated fibroblasts, we will perform gain and loss of function studies on these genes to mechanistically link their chromatin structure, transcription, and phenotype. This project will have long-term basic and translational impacts, with the end goal of shaping the Applicant into an independent scientist within 3 years.