Defining the Multi-Omics Landscape of Phospholamban-induced Cardiomyopathy for Precision Medicine

About This Grant

PROJECT SUMMARY/ABSTRACT Dilated cardiomyopathy (DCM) is a leading cause of heart failure, with approximately 40% of DCM cases linked to pathogenic genetic variants. Despite advances in genetic testing, there remains a major knowledge gap in how specific variants contribute to the multifaceted clinical manifestations of DCM. A notable example is a pathogenic variant in the phospholamban (PLN) gene resulting from deletion of arginine 14 (PLN-R14del). PLN induces DCM characterized by prominent ventricular arrhythmias and highly variable phenotypes, ranging from severe, early-onset disease to lifelong asymptomatic carriage. Such variability makes it challenging to establish genotype-phenotype relationships in PLN-R14del carriers, highlighting the urgent need for new technologies to bridge this gap. Advances in omics technologies are revolutionizing precision medicine. Among omics methods, top-down proteomics has emerged as a powerful technology for studying post-translational modification (PTMs), genetic variants, and splicing isoforms (collectively known as “proteoforms”). Top-down proteomics is ideally positioned for studying complex genetic diseases like PLN-R14del DCM, providing direct evidence of how genetic mutations affect proteoform compositions and linkage to function and phenotype, thereby bridging genotype-phenotype gap. Our preliminary data show that the PLN-R14del variant is associated with unique changes in cardiac proteoforms, including alterations in critical Ca2+-handling, contractile, and metabolic proteoforms, in both human patient tissue and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Hence, we hypothesize that dysregulation of Ca2+-handling, contractile, and metabolic proteoforms and the corresponding pathways contribute to variability in disease phenotypes and expressivity in PLN-R14del carriers. To test this hypothesis, we will employ a systems biology approach featuring novel multi- omics, incorporating proteomics, metabolomics and lipidomics, in combination with human clinical samples and patient-derived hiPSC-CM cellular models. Specifically, we will carry out multi-omics analysis of myocardial tissue from patients with PLN-R14del DCM, compared with genotype-negative DCM and nonfailing donor tissue as controls. The findings from the omics analyses will be further integrated with clinical data to develop patient- specific disease signatures in PLN-R14del carriers. We will also determine differences between symptomatic and asymptomatic PLN-R14del carriers through multi-omics analysis of patient-derived and isogenic control hiPSC-CMs and link them to changes in contractility/metabolism using functional assays. We will further connect the PLN-R14del variant mechanistically to proteoform alterations and their functional outcomes using gain- and loss-of-function approaches. Successful completion of the proposed study will provide new insights into the mechanisms underlying cardiac dysfunction in PLN-R14del, as well as bridge the genotype-phenotype knowledge gap in familial DCM to improve risk-stratification in variant carriers, advance our understanding of genetic diseases, and facilitate the development of targeted treatments towards precision medicine.