Human pluripotency is initiated and preserved by a unique subset of founder cells [single-cell RNA-sequencing]

The assembly of organized colonies is the earliest manifestation in the derivation or induction of pluripotency in vitro. However, the necessity and origin of this assemblance is unknown. Here, we identify human pluripotent founder cells (hPFCs) that initiate as well as preserve and establish pluripotent stem cell (PSC) cultures. PFCs are marked by N-cadherin expression (NCAD+) and reside exclusively at the colony boundary of primate PSCs. Functional analysis demonstrated hPFCs harbor the clonogenic capacity of PSC cultures, and emerge prior to commitment events or phenotypes associated with pluripotent reprogramming. Comparative single cell analysis with pre- and post-implantation primate embryos revealed hPFCs share hallmark properties with primitive endoderm (PrE) and can be regulated by non-canonical Wnt signaling. Uniquely informed by primate embryo organization in vivo, our study defines a subset of founder cells uniquely involved in the establishment pluripotent state. Droplet-based single-cell RNA-sequencing of bulk- and NCAD-positive hESCs. Two lines of hESCs (H1 and H9) were loaded to the Chromium Controller as mixtures and then computationally segregated based on coverage of the sex chromosomes after sequencing and alignment.