New Tricks with Old Dogs: Computational Identification and Experimental Validation of New miRNA-mRNA Regulation in hiPSC-CMs

Cardiovascular disease is still the leading cause of morbidity and mortality worldwide. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have become a valuable widespread in vitro model to study cardiac disease. Herein, we employ the hiPSC-CM model to identify novel miRNA-mRNA interaction partners during cardiac differentiation and beta-adrenergic stress. Whole transcriptome and small RNA sequencing data were combined to identify novel miRNA-mRNA interactions. Briefly, mRNA and miRNA expression profiles were integrated with miRNA target predictions to identify significant statistical dependencies between a miRNA and its candidate target set. We show by experimental validation that our approach discriminates true from false miRNA target predictions. Thereby, we identified several differentially expressed miRNAs and focused on the two top candidates: miR-99a-5p in the context of cardiac differentiation and miR-212-3p in the context of beta-adrenergic stress. We validated some target mRNA candidates by 3 ' UTR luciferase assays as well as in transfection experiments in the hiPSC-CM model system. Our data show that iPSC-derived cardiomyocytes and computational modeling can be used to uncover new valid miRNA-mRNA interactions beyond current knowledge.

Automated summary

Cardiovascular disease is the leading cause of morbidity and mortality worldwide. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have been used as an in vitro model to study cardiac disease and identify novel miRNA-mRNA interactions. By integrating whole transcriptome and small RNA sequencing data, we discovered new miRNA-mRNA interactions. Experimental validation showed that our approach can distinguish true from false miRNA target predictions.