Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal

Abstract

Archetypal human pluripotent stem cells (hPSC) are widely considered to be equivalent in developmental status to mouse epiblast stem cells, which correspond to pluripotent cells at a late post-implantation stage of embryogenesis. Heterogeneity within hPSC cultures complicates this interspecies comparison. Here we show that a subpopulation of archetypal hPSC enriched for high self-renewal capacity (ESR) has distinct properties relative to the bulk of the population, including a cell cycle with a very low G1 fraction and a metabolomic profile that reflects a combination of oxidative phosphorylation and glycolysis. ESR cells are pluripotent and capable of differentiation into primordial germ cell-like cells. Global DNA methylation levels in the ESR subpopulation are lower than those in mouse epiblast stem cells. Chromatin accessibility analysis revealed a unique set of open chromatin sites in ESR cells. RNA-seq at the subpopulation and single cell levels shows that, unlike mouse epiblast stem cells, the ESR subset of hPSC displays no lineage priming, and that it can be clearly distinguished from gastrulating and extraembryonic cell populations in the primate embryo. ESR hPSC correspond to an earlier stage of post-implantation development than mouse epiblast stem cells.

Capture of mouse and human stem cells with features of formative pluripotency

“…In human, FS cells appear related to a somewhat earlier stage of postimplantation epiblast than conventional hPSCs. However, conventional hPSCs are not equivalent to EpiSCs (Lau et al, 2020), and the differences from FS cells are less marked.…”

“…At the transcriptome level human FS cells differ from populations of conventional hPSCs cultured in E8 or other conditions, but these differences are relative rather than absolute. Heterogeneity and hierarchical substructure has been described in hPSC cultures (Allison et al, 2018;Hough et al, 2009;Hough et al, 2014;Lau et al, 2020;Nakanishi et al, 2019) and we cannot exclude the presence of formative stem cells at some frequency. Human FS cells and conventional hPSCs may be a continuum spanning stages of postimplantation epiblast.…”

“…Neither of those functional criteria are applicable in the human context. Conventional hPSCs share some features with EpiSCs but do not appear to be direct equivalents (Lau et al, 2020;Rossant and Tam, 2017). Notably they can be induced to form primordial germ celllike cells (Irie et al, 2015;Sasaki et al, 2015).…”

Transposable Element-Gene Splicing Modulates the Transcriptional Landscape of Human Pluripotent Stem Cells

“…Analysis of the expression of G1, S and G2/M-specific genes indicated that clusters 0 and 1 had higher expression of G2/M and proliferative genes (Fig. 6D, E), suggesting these are highly proliferative cells identified previously (Nguyen et al 2018;Lau et al 2020), positive for EPCAM, CD9 and PODXL (GCTM2) (Fig. 6E, and Supplemental Fig.…”

Organization of the Pluripotent Genome

“…4). Indeed, a recent study has shown that subpopulations of human pluripotent stem cells with high capacities for self-renewal have greater chromatin accessibility at regions of pluripotency TF binding (Lau et al 2020). Moreover, evidence from zebrafish embryos indicates that TFs are in passive competition with core histones for bind-ing to DNA, and the nuclear ratio between histones and DNA-binding factors is important for the onset of zygotic transcription (Joseph et al 2017).…”