Spatio-Temporal Analysis of Human Preimplantation Development Reveals Dynamics of Epiblast and Trophectoderm Specification

Recent technological advances such as single-cell (sc) RNAseq and CRISPR-CAS9-mediated knock-out have allowed an unprecedented access to processes orchestrating human preimplantation development. However, the sequence of events which occur during human preimplantation development are still unknown. In particular, the timing of the first human lineage specification, the process by which the morula cells acquire a specific fate, remains elusive. Here, we present a mouse and human preimplantation development model based on transcriptomic pseudotime modelling of scRNAseq biologically validated by spatial information and precise time-lapse staging. We show that in human, trophectoderm (TE) and inner cell mass (ICM) specification in not complete until the B3 blastocyst stage. This reveals a delay with the mouse first specification. We identified novel markers enabling precise staging of human preimplantation embryos: IFI16, associated to the developed epiblast (EPI) and NR2F2, associated with TE development. Strikingly, NR2F2 positive TE cells arise from the polar side, shortly after specification, supporting a model of faster polar TE development leading to polar implantation in the endometrium. Altogether, our study unravels preimplantation lineage specification in human embryos and provides a browsable resource for mapping spatio-temporal events orchestrating human preimplantation development.