Systems Biology Approaches To Identify Novel Drugs and Mechanisms Regulating Cardiomyocyte Size and Shape 2 views

Heart failure progression is driven by pathological cardiomyocyte remodeling, yet the molecular pathways controlling cell size and those regulating cell shape are distinct, a divergence that current therapies do not adequately address. This dissertation applies a systems pharmacology framework integrating proteomics, computational network modeling, high-content phenotypic screening, and pharmacological validation to define how cardiomyocyte size and shape are independently regulated across three biological contexts: growth factor signaling, genetic mutation, and epigenetic state. In Chapter 2, reverse phase protein array (RPPA) proteomics across four hypertrophic ligands, combined with partial least squares regression (PLSR) modeling, revealed that PI3K/AKT and MAPK signaling modules differentially predict cardiomyocyte size versus shape. Neuregulin-1 uniquely induced cardiomyocyte elongation, quantified using the newly developed Feret Elongation metric, in neonatal rat and human iPSC-derived cardiomyocytes. PI3K activity was required for both elongation and area expansion, whereas p38 selectively mediated cell area growth. A logic-based signaling network model incorporating DUSP feedback reproduced these dynamics and provided a mechanistic explanation for how cell size and shape can diverge downstream of the same ligand stimulus. In Chapter 3, a CRISPR-engineered MYBPC3W1082* mouse model recapitulated hallmarks of hypertrophic cardiomyopathy including ventricular hypertrophy, sarcomere disarray, and fibrosis. Virtual knockdown screening using a mutation-specific signaling network identified the PI3K/AKT/mTOR axis as the dominant regulator of cardiomyocyte mass and nominated rapamycin as a therapeutic candidate. Rapamycin attenuated hypertrophy in both cardiomyocytes and mice, and retrospective analysis of FDA adverse event reports further indicated that sirolimus is associated with reduced hypertrophic cardiac events in patients. In Chapter 4, a high-content screen of 276 epigenetic compounds demonstrated that histone deacetylase (HDAC) inhibitors produce six distinct morphological phenotypes rather than a uniform antihypertrophic response. Mocetinostat induced concentric antihypertrophic remodeling, whereas trichostatin A promoted eccentric elongation. Transcriptomic profiling revealed that remodeling outcomes are heterogenous and do not depend on the inhibitor class alone. Together, these studies demonstrate that cardiomyocyte remodeling is governed by the intersection of signaling, genetic, and epigenetic context, and show that integrated computational and experimental frameworks can identify and validate therapeutic targets for heart disease.

PHD (Doctor of Philosophy)

Cardiac hypertrophy; Systems biology; Modeling

English

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2026-04-24