A developmental coordinate of pluripotency among mice, monkeys and humans

Abstract

The epiblast (EPI) is the origin of all somatic and germ cells in mammals, and of pluripotent stem cells in vitro. To explore the ontogeny of human and primate pluripotency, here we perform comprehensive single-cell RNA sequencing for pre- and post-implantation EPI development in cynomolgus monkeys (Macaca fascicularis). We show that after specification in the blastocysts, EPI from cynomolgus monkeys (cyEPI) undergoes major transcriptome changes on implantation. Thereafter, while generating gastrulating cells, cyEPI stably maintains its transcriptome over a week, retains a unique set of pluripotency genes and acquires properties for 'neuron differentiation'. Human and monkey pluripotent stem cells show the highest similarity to post-implantation late cyEPI, which, despite co-existing with gastrulating cells, bears characteristics of pre-gastrulating mouse EPI and epiblast-like cells in vitro. These findings not only reveal the divergence and coherence of EPI development, but also identify a developmental coordinate of the spectrum of pluripotency among key species, providing a basis for better regulation of human pluripotency in vitro.

Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos

“…Recently, two groups reported their single-cell transcriptomic analyses of mouse early post-implantation embryos (21,27,29). However, characteristics of the pre-MEN cells and the divergence between ME and DE cells were not included in these studies.…”

“…S6A). In another study by Nakamura et al (29), 16 cells from E5.5 embryos and 18 cells from E6.5 embryos were sequenced and analyzed. Diffusion map analysis showed that some of Nakamura's embryonic cells (all expressing T) were also similar to our ME cells, although the size of their samples was small, and no cells were similar to our DE cells (supplemental Fig.…”

“…Our study extends this issue to an earlier stage (E6.5) and uncovers more aspects of signals and transcription factors that may govern the segregation of EXEM cells and embryonic ME cells. Finally, we examined whether EXEM cells could be identified from the Scialdone et al (27) or the Nakamura et al (29) E6.5 ME cells. Our analysis showed that no EXEM cells were identified from the Scialdone et al (27) dataset (supplemental Fig.…”

“…Thus far, the single-cell techniques have been used to reveal pluripotency state transition and lineage segregation of embryonic stem cells and distinct cell types of preimplantation embryos (2)(3)(4)(5)(22)(23)(24)(25)(26). More recently, the technology was also used to decipher the mesodermal lineage diversification toward the hematopoietic system in the post-implantation embryo (27,28), and to compare the pluripotency state between preimplantation and post-implantation embryos (5,29). However, it still remains a challenge to obtain gene expression profiles of embryonic cells that specify earliest in the EPI and to know how they segregate into ME and DE in the PS in vivo.…”

Epigenetic foundations of pluripotent stem cells that recapitulate in vivo pluripotency

“…Naive human ES cells were similarly established directly from human blastocysts. 83 Consistent with ICM-like pluripotency, human ES cells in these conditions display global DNA hypomethylation and the gene expression patterns of naive markers and transposons, which are reminiscent of preimplantation human embryos [84][85][86] ( Figure 5). Of particularly note, inactive X chromosome becomes active in naive-like female cells in vitro, suggesting that reactivation of X chromosome occurs during naive conversion 84,87,88 (Figure 5).…”