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Identification of Human Pluripotent Founder Cells

Review of “Human Pluripotency Is Initiated and Preserved by a Unique Subset of Founder Cells” from Cell by Stuart P. Atkinson

The architecture and spatial organization of cell colonies [1, 2] and transcriptional heterogeneity within the colony [3, 4] affect the functional characteristics of human pluripotent stem cells (hPSC) in vitro; a paradigm with similarities to the early development of the mammalian embryo [5]. Guided by this insight, researchers led by Mickie Bhatia (McMaster University, Hamilton, Canada) assessed the link between hPSC spatial organization and pluripotency, and in doing so, identified a subset of hPSCs that surround and define colony boundaries. Fascinatingly, this subset of N-cadherin positive hPSCs function in the initiation and establishment of pluripotency and subsequent self-renewal [6], and have now been postulated as human pluripotent “founder” cells in a recent Cell article.

Nakanishi et al. first undertook an immunocytochemical screen for cell surface antigens that distinguish colony cells from non-colony cells using a range of hPSCs and culture conditions. In doing so, the team discovered that N-cadherin positive cells created a perimeter edge in established colonies of hPSCs and also iPSCs derived from non-human primate fibroblasts. Characterization of N-cadherin positive hPSCs by droplet-based single-cell RNA sequencing following isolated by fluorescence-activated cell sorting revealed a distinctive transcriptional signature that included transcripts related to early development and pluripotency. 

Fascinatingly, the authors then demonstrated that N-cadherin positive border-resident hPSCs function as master controllers of hPSC cultures in that they harbor hPSC colony-initiating capacity, possess unrestricted and unbiased lineage potential, and initiate pluripotent colony formation during the reprogramming of somatic cells to induced pluripotent stem cells. For this reason, the team named these cells human pluripotent founder cells.

Interestingly, single-cell comparisons of human pluripotent founder cells with cells of the pre- and post-implantation primate embryos revealed unexpected, yet broad similarities to cells of the primitive endoderm rather than the epiblast, and that primitive endoderm-specification associated genes (such as GATA6 and DAB2) governed human pluripotent founder cell self-renewal and the earliest stages of pluripotent initiation. Further wide-ranging analyses based on the transcriptional data generated then helped to establish the non-canonical Wnt signaling pathway as a critical regulator of human pluripotent founder cells, human pluripotent reprogramming, and establishment of pluripotency.

This study, which uncovers previously unappreciated cellular origins and function of in vitro pluripotency, creates multiple fascinating possibilities, including the prospect of precisely tuning non-canonical Wnt signaling during hPSC culture to generate higher numbers of human pluripotent founder cells and improve the efficiency of directed lineage differentiation strategies. 

For more on the fall out of this fascinating new study, stay tuned to the Stem Cells Portal!


  1. Warmflash A, Sorre B, Etoc F, et al., A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nature Methods 2014;11:847.
  2. Nazareth EJP, Ostblom JEE, Lücker PB, et al., High-throughput fingerprinting of human pluripotent stem cell fate responses and lineage bias. Nature Methods 2013;10:1225.
  3. Hough Shelley R, Thornton M, Mason E, et al., Single-Cell Gene Expression Profiles Define Self-Renewing, Pluripotent, and Lineage Primed States of Human Pluripotent Stem Cells. Stem Cell Reports 2014;2:881-895.
  4. Drukker M, Tang C, Ardehali R, et al., Isolation of primitive endoderm, mesoderm, vascular endothelial and trophoblast progenitors from human pluripotent stem cells. Nature Biotechnology 2012;30:531.
  5. Irvine KD and Rauskolb C, Boundaries in Development: Formation and Function. Annual Review of Cell and Developmental Biology 2001;17:189-214.
  6. Nakanishi M, Mitchell RR, Benoit YD, et al., Human Pluripotency Is Initiated and Preserved by a Unique Subset of Founder Cells. Cell 2019;177:910-924.e22.