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MicroRNAs (miRNAs) are known to be crucial players in governing the differentiation of human induced pluripotent stem cells (hiPSCs). Despite their utter importance, identifying key lineage specifiers among the myriads of expressed miRNAs remains challenging. We believe that the current practice in mining miRNA specifiers via delineating dynamic fold-changes only is inadequate. Our study, therefore, provides evidence to pronounce “lineage specificity” as another important attribute to qualify for these lineage specifiers. Adopted hiPSCs were differentiated into representative lineages (hepatic, nephric and neuronal) over all three germ layers whilst the depicted miRNA expression changes compiled into an integrated atlas. We demonstrated inter-lineage analysis shall aid in the identification of key miRNAs with lineage-specificity, while these shortlisted candidates were collectively known as “lineage-specific miRNAs”. Subsequently, we followed through the fold-changes along differentiation via computational analysis to identify  miR-192  and  miR-372-3p , respectively, as representative candidate key miRNAs for the hepatic and nephric lineages. Indeed, functional characterization validated that  miR-192  and  miR-372-3p  regulate lineage differentiation via modulation of the expressions of lineage-specific genes. In summary, our presented miRNA atlas is a resourceful ore for the mining of key miRNAs responsible for lineage specification.

Comparison of multi-lineage differentiation of hiPSCs reveals novel miRNAs that regulate lineage specification