Comprehensive miRNA profiling of human naïve, intermediate and primed pluripotent stem cells

Naïve human pluripotent stem cells (hPSC) represent an earlier time-point in embryogenesis than conventional, 'primed' hPSCs. We present a comprehensive miRNA profiling of naïve-to-primed transition in hPSC, a process resembling aspects of early in vivo embryogenesis. We identify miR-143-3p and miR-22-3p as markers of the naïve state and miR-363-5p, several members of the miR-17 family, miR-302 family as primed markers. We uncover that miR-371-373 are highly upregulated in naïve hPSC. MiR-371-373 are the human homologs of the mouse miR-290 family, which are the most highly expressed miRNAs in mPSC. This aligns with the consensus that naïve hPSC resemble mPSC, showing that the absence of miR-371-373 in conventional hPSC is due to cell state rather than a species difference. Overall design: To investigate miRNAs involved in the differentiation of naïve hPSC to primed hPSC, the effectiveness of the in vitro differentiation process itself was first assessed, using the directly derived naïve HNES1 and HNES2 cell lines. Differentiation was instigated in three separately cultured replicates of each of HNES1 and HNES2 naïve cells, plating them on geltrex and switching medium to E8 after 48 hours, thereby removing potential variability introduced if splitting the cells. The time points were chosen to capture the exit from naïve pluripotency, with a final late time point to ensure complete priming of the cells. Day 42 was chosen for the final time point since the cells had by then regained the ability to differentiate using standard primed protocols. Total RNA samples from naïve cells cultured above (HNES1 and HNES2, each cultured separately in biological triplicates) at day 0, during the transition (day 2) and when fully primed (day 42), were analysed by miRNAseq.