Gene Modulation of Acetylation Modifiers to Reveal Regulatory Links to Human Cardiac Electromechanics

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PROJECT ABSTRACT Epigenetic regulation is critical for cardiac electromechanics and pathology. Epigenetic modulators, such as histone deacetylases (HDACs), are known master regulators of gene expression and influence cardiac function through chromatin remodeling, direct action on transcription factors (TFs), and action on cytoskeletal and contractile proteins, among others. Recently, novel pharmacological agents, HDAC inhibitors, have been developed as treatments for cancer and immune diseases, driving an interest in robust characterization of HDAC control in cardiac function. Our preliminary experiments focused on computational modeling of RNAi-informed transcriptomic data in human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CM) but saw limitations in knockdown efficiency and loss-of-function-only modulation using siRNAs. To extend and improve this work, we propose an experimental approach based on bidirectional perturbation (repression/activation) of individual HDAC genes in hiPSC-CM by CRISPR interference and activation (CRISPRi/a). Transcriptomic analysis of these samples will inform computational gene regulatory network (GRN) inference to model relationships between HDACs, TFs, and cardiac ion channels. GRN-predicted relationships will be validated by all-optical electromechanical assays measuring voltage, calcium, and contraction traces in hiPSC-CM. An iterative approach will allow feedback from functional experiments to refine our computational models. Such studies will advance our understanding of how certain HDACs drive electrophysiological phenotypes in the heart, which is critical in the fields of cardiac injury, cardiac therapeutics, and cardio-oncology.