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Open AccessJournal ArticleDOI

A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre.

TLDR
In this article, the authors identify a group of asymmetrically positioned extra-embryonic hypoblast cells expressing inhibitors of BMP, NODAL and WNT signalling pathways and suggest that these cells can act as the anterior singalling centre to pattern the epiblast.
Abstract
Following implantation, the human embryo undergoes major morphogenetic transformations that establish the future body plan. While the molecular events underpinning this process are established in mice, they remain unknown in humans. Here we characterise key events of human embryo morphogenesis, in the period between implantation and gastrulation, using single-cell analyses and functional studies. First, the embryonic epiblast cells transition through different pluripotent states and act as a source of FGF signals that ensure proliferation of both embryonic and extra-embryonic tissues. In a subset of embryos, we identify a group of asymmetrically positioned extra-embryonic hypoblast cells expressing inhibitors of BMP, NODAL and WNT signalling pathways. We suggest that this group of cells can act as the anterior singalling centre to pattern the epiblast. These results provide insights into pluripotency state transitions, the role of FGF signalling and the specification of anterior-posterior axis during human embryo development.

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Journal ArticleDOI

Single-cell transcriptomic characterization of a gastrulating human embryo.

TL;DR: In this paper, the authors characterized the single-cell transcriptional profiles of an entire gastrulating human embryo, staged to be between 16 and 19 days after fertilization, and identified primordial germ cells, red blood cells and various mesodermal and endodermal cell types.
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Early human embryonic development: Blastocyst formation to gastrulation.

TL;DR: Rossant and Tam as mentioned in this paper discuss new insights into human embryogenesis gathered from successes in culturing human embryos in vitro and stem-cell-based embryo models, and outline what questions still need answering.
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Spatial profiling of early primate gastrulation in utero

TL;DR: In this article , spatial transcriptomics and stem-cell-based embryo models were used to reveal the molecular code of lineage specification in the primate embryo and provide an in vivo reference to decipher human development.
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The exploration of pluripotency space: Charting cell state transitions in peri-implantation development.

TL;DR: In this article, the authors examined these recent findings in light of our knowledge of peri-implantation mouse and human development, and considered the implications of this work for deriving human embryo models from pluripotent cells.
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In vitro attachment and symmetry breaking of a human embryo model assembled from primed embryonic stem cells.

TL;DR: In this article , a pre-formed polarized epithelial epiblast and extra-embryonic cells are assembled into a structure that mimics the dish-attached human embryo, and the model attaches in vitro and, in the absence of exogenous morphogens, breaks anteroposterior symmetry.
References
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Journal ArticleDOI

NIH Image to ImageJ: 25 years of image analysis

TL;DR: The origins, challenges and solutions of NIH Image and ImageJ software are discussed, and how their history can serve to advise and inform other software projects.
Journal ArticleDOI

Comprehensive Integration of Single-Cell Data.

TL;DR: A strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities.
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Integrating single-cell transcriptomic data across different conditions, technologies, and species.

TL;DR: An analytical strategy for integrating scRNA-seq data sets based on common sources of variation is introduced, enabling the identification of shared populations across data sets and downstream comparative analysis.
Journal ArticleDOI

Near-optimal probabilistic RNA-seq quantification

TL;DR: Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases, which removes a major computational bottleneck in RNA-seq analysis.
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