CDK8/19 small molecule inhibition promotes naïve features in human and mouse pluripotent stem cells II

Pluripotent stem cells (PSCs) can transition between cell states in vitro, closely reflecting developmental changes in the early embryo. PSCs can be stabilized in their naive state by blocking extracellular differentiation stimuli, particularly FGF5 MEK signaling. Here, we report that multiple features of the naive state in human and mouse PSCs can be recapitulated without affecting FGF-MEK-signaling. Mechanistically, chemical inhibition of CDK8 and CDK19 kinases (CDK8/19i) removes their ability to repress the Mediator complex at enhancers. Thus CDK8/19i increases Mediator-driven recruitment of RNA Pol II to promoters and enhancers. This efficiently stabilizes the naive transcriptional program, and confers resistance to enhancer perturbation by BRD4 inhibition. Moreover, naive pluripotency during embryonic development coincides with reduction in CDK8/19. We conclude that global hyperactivation of enhancers drives naive pluripotency, and this can be captured in-vitro by inhibiting extracellular FGF-MEK-signaling, or downstream, by CDK8/19i. These principles may apply to other contexts of cellular plasticity. Overall design: Five human pluripotent stem cell lines (PSCs) were cultured in two conditions ("Primed" vs "CDK8/19i") for long-term/10passages, and then transcriptomic differences between the two groups were assessed by RNAseq. Culture conditions were either standard primed conditions ("Primed" = mTeSR media with FGF2 and TGFb1, feeder-free, on matrigel), or including additional media supplementation with recombinant human LIF (20 ng/ml) and CDK8/19-small molecule inhibitor at 0,4 mM (= "CDK8/19i" or "8i"). The five cell lines were H1, D2#2, D2#4, CB5 and WIBR3.