Abstract Body: Introduction: The immaturity of pluripotent stem cell (PSC)-derived cells remains a major barrier for their application in disease modeling, drug screening, and regenerative medicine. PSC-derived cardiomyocytes (PSC-CMs), in particular, exhibit fetal-like structural and functional properties, limiting their reliability as in vitro models and raising arrhythmogenic risks in therapeutic settings. To address this, we sought to identify microRNAs (miRNAs) that universally drive maturation-related transcriptomic changes across organs, as these may serve as more effective tools to promote PSC-CM maturation.
Methods: To investigate whether certain microRNAs (miRNAs) are commonly expressed across different tissues during organ maturation, we conducted small RNA sequencing on mouse brain, heart, and liver—each representing one of the three germ layers—at five embryonic and postnatal time points. We clustered miRNAs by their temporal expression patterns using the Mfuzz R package, and we compared temporally upregulated clusters to identify shared miRNAs. We predicted potential target genes of the miRNAs in the heart by intersecting predicted targets from the miRmap in silico tool with downregulated genes from published cardiac transcriptomics data.
Results: Our analysis identified five shared miRNAs (miR-22, miR-26a-1, miR-29a, miR-29c, and miR-378c) that showed a consistent increase in expression from embryonic day 13 to postnatal day 28 across the mouse brain, heart, and liver. In addition, we identified 1,286 predicted target genes in the heart for these miRNAs. Gene Ontology analysis indicated that these targets are associated with cell cycle regulation and metabolic processes, suggesting a potential role for these miRNAs in driving cell cycle exit and metabolic maturation.
Conclusions: By identifying candidate miRNAs regulating organ-wide maturation, our study provides potential tools that could enhance maturation of PSC-CMs and other PSC-derived cell types. Such advancements could improve the accuracy of in vitro models and reduce safety concerns in therapeutic applications, ultimately enhancing their clinical potential.