Epiblast-like stem cells established by Wnt/β-catenin signaling manifest distinct features of formative pluripotency and germline competence

Different formative pluripotent stem cells harboring similar functional properties have been recently established to be lineage neutral and germline competent yet have distinct molecular identities. Here, we show that WNT/β-catenin signaling activation sustains transient mouse epiblast-like cells as epiblast-like stem cells (EpiLSCs). EpiLSCs display metastable formative pluripotency with bivalent cellular energy metabolism and unique transcriptomic features and chromatin accessibility. We develop single-cell stage label transfer (scSTALT) to study the formative pluripotency continuum and reveal that EpiLSCs recapitulate a unique developmental period in vivo, filling the gap of the formative pluripotency continuum between other published formative stem cells. WNT/β-catenin signaling activation counteracts differentiation effects of activin A and bFGF by preventing complete dissolution of naive pluripotency regulatory network. Moreover, EpiLSCs have direct competence toward germline specification, which is further matured by an FGF receptor inhibitor. Our EpiLSCs can serve as an in vitro model for mimicking and studying early post-implantation development and pluripotency transition. [Display omitted] •EpiLSCs are molecularly distinct from other formative pluripotency stem cells•Single-cell stage label transfer (scSTALT) enables integrated pseudotime analysis•WNT activation sustains metastable formative pluripotency of EpiLSCs•EpiLSCs have competence for germline induction with enhanced maturation by PD Luo et al. report mouse epiblast-like stem cells (EpiLSCs) displaying a metastable formative pluripotency and recapitulating a particular developmental period. EpiLSCs serve as an in vitro model for post-implantation development and pluripotency transition.