Alternative splicing dynamics during human cardiac development in vivo and in vitro

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. Alternative splicing (AS), a crucial mechanism for regulating gene expression during development, plays a pivotal role in cardiac differentiation and maturation. However, the extent to which iPSC-CMs recapitulate native cardiac splicing patterns remains poorly understood. Here, we provide a comprehensive temporal map of AS regulation during human cardiac development. In addition to the major splicing changes occurring perinatally, we identify finely tuned prenatal splicing transitions. While iPSC-CMs globally resemble the prenatal heart transcriptome, their splicing profiles are heterogeneous, with some splicing patterns mirroring the early embryonic tissue and others aligning with later stages. Moreover, we uncover altered splicing events in iPSC-CMs, including mis-splicing of splicing factors. In conclusion, we present a resource of AS dynamics throughout human cardiac development and a catalog of splicing markers to assess cardiomyocyte maturation in vitro . Our findings provide critical insights into the limitations of iPSC-CM models and their utility in cardiovascular research.