A spatially resolved single cell atlas of human gastrulation

Abstract

Gastrulation is the fundamental process during the embryogenesis of all multicellular animals through which the basic body plan is first laid down. It is pivotal in generating cellular diversity coordinated with spatial patterning. Gastrulation in humans occurs in the third week following fertilization. Our understanding of this process in humans is extremely limited, and based almost entirely on experimental models. Here, we characterize in a spatially resolved manner the single cell transcriptional profile of an entire gastrulating human embryo approximately 16 to 19 days after fertilization. We used these data to provide the first unequivocal demonstration that human embryonic stem cells represent the early post implantation epiblast. We identified both primordial germ cells and red blood cells, which had never been characterized so early during human development. Comparison with mouse gastrula transcriptomes revealed many commonalities between the human and mouse but also several key differences, particularly in FGF signaling, that we validated experimentally. This unique dataset offers a unique glimpse into a central but generally inaccessible stage of our development, provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cells in vitro.

Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage

“…A recent study shows that both genes may be dispensable for hPGCLC specification ( Hancock et al., 2020 ); however, further work is needed to establish the role of these naive pluripotency genes in germline development. Similarly, PRDM14 , which is not detected in CS7 hPGCs ( Tyser et al., 2020 ), is only detectable in some gonadal pPGCs, suggesting that it may not have an essential role during pPGC specification ( Figures 1 B and 1F; Kobayashi et al., 2017 ). Recent evidence shows that PRDM14 may have a role in maintenance of hPGCs after specification ( Sybirna et al., 2020 ).…”

“…Previous studies have shown that, after their induction in posterior early-PS Epis, the PGC cluster localizes at the embryonic and extraembryonic border in pig pre-somatic-stage embryos ( Kobayashi et al., 2017 ; Wolf et al., 2011 ). Similarly, in a gastrulating CS7 human embryos, hPGCs have been suggested to emerge from the PS and are set apart from nascent mesoderm and other lineages ( Tyser et al., 2020 ). Importantly, these cell types are induced by BMP signaling, which is detected in the posterior end of the pig embryo from E12 onward ( Valdez Magaña et al., 2014 ; Yoshida et al., 2016 ).…”

“…Interestingly, low and fluctuating SOX17 expression is also observed in early hPGCs in CS7 human embryos, whereas the endoderm lineage shows consistent and high SOX17. Low and fluctuating SOX17 expression in early pPGCs and hPGCs might reflect a conserved mechanism to regulate gene dosage to prevent expression of endoderm genes in hPGCs and pPGCs ( Irie et al., 2015 ; Kobayashi et al., 2017 ; Tyser et al., 2020 ).

Figure 1 Transcriptional profile of pPGCs and comparison with hPGCs (A) Bright-field top view image of a pig embryo (left) and diagrammatic representation (right) showing key structures.

…”

“…To investigate the conservation of germline development in detail, we compared the expression profiles of pPGCs, hPGCs, and cyPGCs by integrating scRNA-seq datasets ( Li et al., 2017 ; Sasaki et al., 2016 ; Tyser et al., 2020 ). Pre migratory (E14) pPGCs cluster with E13–E20 cyPGCs (ePGCs), whereas E31 pPGCs clustered with E36–E55 cyPGCs (lPGCs) ( Figure 1 D).…”

“…Indeed, the initial studies of the critical factors and the mechanism of hPGC specification from in vitro models were confirmed by direct observations of pPGC specification in gastrulating pig embryos, suggesting that studies of the two species will be mutually informative. Importantly, investigations of very early hPGCs are exceptional ( Tyser et al., 2020 ), especially during the critical period of weeks 2–4 of human development, when they are essentially inaccessible. Our observations of pPGCs over this critical period, covering specification and initiation of epigenetic reprogramming, likely apply to hPGCs.…”