Proteomic characterization of human iPSC-derived cardiomyocytes

Cardiomyocytes differentiated in vitro from human induced pluripotent stem cells (iPSC-CMs) are increasingly used in studies of disease mechanisms, drug development, toxicity testing, and regenerative medicine. However, the extent to which iPSC-CMs recapitulate native cardiac gene expression programs, at both the splicing and protein levels, remains poorly understood. We investigated the alternative splicing profiles of in vitro differentiated iPSC-CMs in comparison to fetal and adult heart samples. To examine whether splicing isoforms identified in RNA-seq datasets give rise to proteins, we generated a comprehensive proteomic dataset of iPSC-CMs. Integration of RNA and protein datasets enabled the detection of isoform-specific peptides, demonstrating translation of selected alternatively spliced transcripts.