Integrated pseudotime analysis of human preimplantation embryo single-cell transcriptomes reveals the dynamics of lineage specification Graphical abstract Highlights d Distinct trophectoderm/epiblast signatures arise at the B2-B3 blastocyst stages d IFI16 is broadly expressed in the ICM and then restricted to epiblast after implantation d NR2F2 arises from the polar TE in late blastocysts and then spreads to all TE cells

Induced pluripotent stem cells (iPSCs) have considerably impacted human developmental biology and regenerative medicine, notably because they circumvent the use of cells of embryonic origin and offer the potential to generate patient-specific pluripotent stem cells. However, conventional reprogramming protocols produce developmentally advanced, or primed, human iPSCs (hiPSCs), restricting their use to post-implantation human development modeling. Hence, there is a need for hiPSCs resembling preimplantation naive epiblast. Here, we develop a method to generate naive hiPSCs directly from somatic cells, using OKMS overexpression and specific culture conditions, further enabling parallel generation of their isogenic primed counterparts. We benchmark naive hiPSCs against human preimplantation epiblast and reveal remarkable concordance in their transcriptome, dependency on mitochondrial respiration and X-chromosome status. Collectively, our results are essential for the understanding of pluripotency regulation throughout preimplantation development and generate new opportunities for disease modeling and regenerative medicine.

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