Single-cell analysis of embryoids reveals lineage diversification roadmaps of early human development

Zheng, Yi; Yan, Robin Zhexuan; Sun, Shiyu; Kobayashi, Mutsumi; Xiang, Lifeng; Yang, Ran; Goedel, Alexander; Kang, Yu; Xue, Xufeng; Esfahani, Sajedeh Nasr; Liu, Yue; Irizarry, Agnes M Resto; Wu, Wei; Li, Yunxiu; Ji, Weizhi; Niu, Yuyu; Chien, Kenneth R.; Li, Tianqing; Shioda, Toshihiro; Fu, Jianping

doi:10.1016/j.stem.2022.08.009

Cited by 25 publications

(20 citation statements)

References 80 publications

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“…In contrast to mice and pig that undergo amniogenesis by folding, humans and non-human primates undergo amniogenesis by cavitation (Chuva de Sousa Lopes et al, 2022; Eakin and Behringer, 2004) and may share similar origin of PGCs. In agreement, hPGCLCs share a common TFAP2A+ progenitor with amnion ectoderm-like cells in EB-differentiation assays (Chen et al, 2019) and hPGCLC formation has been demonstrated in an amniotic sac embryoid model (Zheng et al, 2019; Zheng et al, 2022).…”

Section: Introductionsupporting

confidence: 63%

“…The observation that BME potentiates BMP/SMAD signaling has significance beyond the field of in vitro gametogenesis. BMP4 is widely used in various differentiation protocols and models of early embryogenesis (Simunovic et al, 2019; Warmflash et al, 2014; Zheng et al ., 2019; Zheng et al ., 2022). Moreover, the presence of BME has proved beneficial for the development of somite-like structures in a mouse 3D gastruloid stem-cell model (van den Brink et al, 2020) as well as developing a peri-implantation assay for non-human primates (Yang et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

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Efficient and scalable generation of primordial germ cells in 2D culture using basement membrane extract overlay

Overeem¹,

CHANG²,

Moustakas³

et al. 2022

Preprint

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Current human primordial germ cell like cells (hPGCLCs) differentiation methods from human pluripotent stem cells (hPSCs) are inefficient, and it is challenging to generate sufficient hPGCLCs to optimize in vitro gametogenesis. We present a new differentiation method that uses diluted basement membrane extract (BME) and low BMP4 concentration to efficiently induce hPGCLC differentiation in scalable 2D cell culture. We show that BME overlay potentiated BMP/SMAD signaling, induced lumenogenesis and increased expression of key hPGCLC-progenitor markers such as TFAP2A and EOMES. These findings highlight the importance of (factors in) BME during hPGCLC differentiation, and demonstrate the potential of the BME-overlay method to interrogate the formation of PGCs and amnion in humans as well to investigate the next steps to achieve in vitro gametogenesis.

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Section: Introductionsupporting

confidence: 63%

Section: Discussionmentioning

confidence: 99%

Efficient and scalable generation of primordial germ cells in 2D culture using basement membrane extract overlay

Overeem¹,

CHANG²,

Moustakas³

et al. 2022

Preprint

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“…On the other hand, although the cluster TFAP2A + , which has been reported as the progenitor cell population of the PGCLC in previous studies [5, 6, 57], shows a similar tendency to the cluster NKX1-2 + until day 1, TFAP2A is also highly expressed in the AMLC population after this day, implying that TFAP2A alone cannot identify the PGCLC progenitor cell population. This analysis suggests that NKX1-2 is one of the earliest marker genes of the PGCLC progenitor cell population, and its expression guides the cell population to the PGCLC pathway.…”

Section: Biological Application Of Scegot To Human Pgclc Induction Sy...mentioning

confidence: 69%

“…Notably, we found that TFAP2A is expressed in the PGCLC progenitor cell population (day0.5-1). Previous studies have shown that this gene plays an important role in PGCLC differentiation [5, 6, 57], suggesting that the cell state graph generated from scEGOT has the ability to capture the progenitor cell population of PGCLC differentiation.…”

Section: Biological Application Of Scegot To Human Pgclc Induction Sy...mentioning

confidence: 99%

scEGOT: Single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport

Yachimura,

Wang,

Imoto

et al. 2023

Preprint

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Time-series single-cell RNA sequencing (scRNA-seq) data have opened a door to elucidate cell differentiation processes. In this context, the optimal transport (OT) theory has attracted attention to interpolate scRNA-seq data and infer the trajectories of cell differentiation. However, there remain critical issues in interpretability and computational cost. This paper presents scEGOT, a novel comprehensive trajectory inference framework for single-cell data based on entropic Gaussian mixture optimal transport (EGOT). By constructing a theory of EGOT via an explicit construction of the entropic transport plan and its connection to a continuous OT with its error estimates, EGOT is realized as a generative model with high interpretability and low computational cost, dramatically facilitating the inference of cell trajectories and dynamics from time-series data. The scEGOT framework provides comprehensive outputs from multiple perspectives, including cell state graphs, velocity fields of cell differentiation, time interpolations of single-cell data, space-time continuous videos of cell differentiation with gene expressions, gene regulatory networks, and reconstructions of Waddington's epigenetic landscape. To demonstrate that scEGOT is a powerful and versatile tool for single-cell biology, we applied it to time-series scRNA-seq data of the human primordial germ cell-like cell (human PGCLC) induction system. Using scEGOT, we precisely identified the PGCLC progenitor population and the bifurcation time of the segregation. Our analysis suggests that a known marker gene TFAP2A alone is not sufficient to identify the PGCLC progenitor cell population, but that NKX1-2 is also required. In addition, we found that MESP1 and GATA6 may also be crucial for PGCLC/somatic cell segregation.

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“…In the most recent work by Fu’s lab, they traced the trajectories of lineages that diversify from the epiblast in their PASE model through single-cell RNA analysis. Epiblast-like cells (EPiLC) branched to derive primitive streak-like cells, amniotic-like cells (AMLC) and primordial germinal cell-like cells (PGCLC), whereas exploring germline origins showed a nascent AMLC population that bifurcated into AMLC and PGCLC [ 60 ]. These results suggest that in primates, PGCs are not directly derived from the epiblast or primitive streak.…”

Section: Non-integrated 3d Embryonic Modelsmentioning

confidence: 99%

Pluripotent Stem Cells as a Model for Human Embryogenesis

Ávila-González

Gidi-Grenat

García‐López

et al. 2023

Cells

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Pluripotent stem cells (PSCs; embryonic stem cells and induced pluripotent stem cells) can recapitulate critical aspects of the early stages of embryonic development; therefore, they became a powerful tool for the in vitro study of molecular mechanisms that underlie blastocyst formation, implantation, the spectrum of pluripotency and the beginning of gastrulation, among other processes. Traditionally, PSCs were studied in 2D cultures or monolayers, without considering the spatial organization of a developing embryo. However, recent research demonstrated that PSCs can form 3D structures that simulate the blastocyst and gastrula stages and other events, such as amniotic cavity formation or somitogenesis. This breakthrough provides an unparalleled opportunity to study human embryogenesis by examining the interactions, cytoarchitecture and spatial organization among multiple cell lineages, which have long remained a mystery due to the limitations of studying in utero human embryos. In this review, we will provide an overview of how experimental embryology currently utilizes models such as blastoids, gastruloids and other 3D aggregates derived from PSCs to advance our understanding of the intricate processes involved in human embryo development.

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Single-cell analysis of embryoids reveals lineage diversification roadmaps of early human development

Cited by 25 publications

References 80 publications

Efficient and scalable generation of primordial germ cells in 2D culture using basement membrane extract overlay

Efficient and scalable generation of primordial germ cells in 2D culture using basement membrane extract overlay

scEGOT: Single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport

Pluripotent Stem Cells as a Model for Human Embryogenesis

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