Abstract
ABSTRACTSingle-cell profiling techniques create opportunities to delineate cell fate progression in mammalian development. Recent studies have provided transcriptome data from human pre-implantation embryos, in total comprising nearly 2000 individual cells. Interpretation of these data is confounded by biological factors, such as variable embryo staging and cell-type ambiguity, as well as technical challenges in the collective analysis of datasets produced with different sample preparation and sequencing protocols. Here, we address these issues to assemble a complete gene expression time course spanning human pre-implantation embryogenesis. We identify key transcriptional features over developmental time and elucidate lineage-specific regulatory networks. We resolve post-hoc cell-type assignment in the blastocyst, and define robust transcriptional prototypes that capture epiblast and primitive endoderm lineages. Examination of human pluripotent stem cell transcriptomes in this framework identifies culture conditions that sustain a naïve state pertaining to the inner cell mass. Our approach thus clarifies understanding both of lineage segregation in the early human embryo and of in vitro stem cell identity, and provides an analytical resource for comparative molecular embryology.
Highlights
Three distinct cell lineages are established in the mammalian blastocyst: trophectoderm (TE), which supports uterine implantation and development of the placental epithelia; extraembryonic primitive endoderm (PrE), from which the primary yolk sac is formed; and pluripotent epiblast (EPI), which gives rise to the embryo proper
TE over-representation in single-cell embryo data We embarked on a systematic analysis of single-cell transcriptome data from three human embryo profiling studies that extend to late blastocyst (Yan et al, 2013; Blakeley et al, 2015; Petropoulos et al, 2016)
Cultures of embryo-derived (Guo et al, 2016) and chemically reset (Guo et al, 2017) cells in t2iLGö were correlated with EPI and 5i/L/A cells to a similar extent, but to a lesser extent with PrE. These findings indicate that human Pluripotent stem cells (PSCs) maintained in t2iLGö represent cogent transcriptional counterparts to the naïve epiblast lineage of the human pre-implantation embryo and suggest that 5i/L/A cells represent a mixed EPI/PrE identity
Summary
Three distinct cell lineages are established in the mammalian blastocyst: trophectoderm (TE), which supports uterine implantation and development of the placental epithelia; extraembryonic primitive endoderm (PrE), from which the primary yolk sac is formed; and pluripotent epiblast (EPI), which gives rise to the embryo proper. The pluripotency factor POU5F1 ( known as OCT4) is widely expressed in both early ICM and TE in the early human blastocyst (Niakan and Eggan, 2013). By E6 in human, POU5F1 is downregulated in TE but remains expressed in all cells of the ICM (Chen et al, 2009; Deglincerti et al, 2016; Niakan and Eggan, 2013). ICM cells with high POU5F1 levels often co-express NANOG (Roode et al, 2012; Deglincerti et al, 2016), suggesting a prospective EPI fate. Lower POU5F1 levels correlate with PrEspecific SOX17 expression (Roode et al, 2012; Niakan and Eggan, 2013)
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