Extraembryonic potential of human pluripotency is suppressed by SALL2
Human pluripotent stem cells can exist in naive and primed states that correspond to the pre- and post-implantation epiblast, respectively. We initially sought to identify regulators of the naive-to-primed transition. Analysis of transcriptomic data from human embryos spanning pre-implantation to gastrulation with in vitro hPSC models identified SALL2 as a candidate regulator. Unexpectedly, CRISPR-mediated deletion of SALL2 in blastocyst-derived naive hPSCs, combined with multiomic profiling, showed that SALL2 is dispensable for priming itself. Instead, SALL2 suppresses extraembryonic differentiation during the naive-to-primed transition. Loss of SALL2 increased WNT signaling and diverted cells into BMP-driven trophectoderm-like and FGF-driven primitive endoderm-like trajectories through a WNT-responsive intermediate. Combinatorial signaling perturbation further showed that SALL2 partially buffers reduced FGF2 and TGF-beta signaling. Consistent with this, blastoids generated from partially primed SALL2-/- hPSCs efficiently produced CDX2+ and GATA6+ cells. Together, these findings reveal that naive-to-primed intermediates retain latent extraembryonic competence that is actively restrained by SALL2.