Embryo model completes gastrulation to neurulation and organogenesis

Creators: Amadei, Gianluca; Handford, Charlotte E.; Qiu, Chengxiang; De Jonghe, Joachim; Greenfeld, Hannah; Tran, Martin; Martin, Beth K.; Chen, Dong-Yuan; Aguilera-Castrejon, Alejandro; Hanna, Jacob H.; Elowitz, Michael B.; Hollfelder, Florian; Shendure, Jay; Glover, David M.; Zernicka-Goetz, Magdalena

Abstract

Embryonic stem (ES) cells can undergo many aspects of mammalian embryogenesis in vitro, but their developmental potential is substantially extended by interactions with extraembryonic stem cells, including trophoblast stem (TS) cells, extraembryonic endoderm stem (XEN) cells and inducible XEN (iXEN) cells. Here we assembled stem cell-derived embryos in vitro from mouse ES cells, TS cells and iXEN cells and showed that they recapitulate the development of whole natural mouse embryo in utero up to day 8.5 post-fertilization. Our embryo model displays headfolds with defined forebrain and midbrain regions and develops a beating heart-like structure, a trunk comprising a neural tube and somites, a tail bud containing neuromesodermal progenitors, a gut tube, and primordial germ cells. This complete embryo model develops within an extraembryonic yolk sac that initiates blood island development. Notably, we demonstrate that the neurulating embryo model assembled from Pax6-knockout ES cells aggregated with wild-type TS cells and iXEN cells recapitulates the ventral domain expansion of the neural tube that occurs in natural, ubiquitous Pax6-knockout embryos. Thus, these complete embryoids are a powerful in vitro model for dissecting the roles of diverse cell lineages and genes in development. Our results demonstrate the self-organization ability of ES cells and two types of extraembryonic stem cells to reconstitute mammalian development through and beyond gastrulation to neurulation and early organogenesis.

Additional Information

We thank all members of the M.Z.-G. laboratory for their suggestions throughout this project, and M. Shahbazi and R. Hadas for help and discussions. This project has been made possible through the following grants to M.Z.-G.: NIH Pioneer Award (DP1 HD104575-01), European Research Council (669198), the Wellcome Trust (207415/Z/17/Z), Open Philanthropy/Silicon Valley Community Foundation and Weston Havens Foundation and the Centre for Trophoblast Research. F.H. was supported by the ERC (69566) and the Wellcome Trust (WT108438/C/15/Z). J.D.J. was supported by the Biotechnology and Biological Sciences Research Council. C.E.H. was supported by the Centre for Trophoblast Research, and the Leventis Foundation. A grant from the Paul G. Allen Frontiers Group (Allen Discovery Centre for Cell Lineage Tracing) supported M.Z.-G., M.B.E. and J.S. J.S. is also supported by the National Human Genome Research Institute (1UM1HG011586 to J.S.; R01HG010632 to J.S.) and is an Investigator of the Howard Hughes Medical Institute. M.B.E. is also an Investigator of the Howard Hughes Medical Institute and is supported by an NIH grant (R01 MH116508). H.G. is supported by a Biology and Biological Engineering postdoctoral fellowship from Caltech. D.-Y.C. is supported by a NIH-NRSA postdoctoral fellowship (5F32HD105442). These authors contributed equally: Gianluca Amadei, Charlotte E. Handford. Contributions. G.A. and C.E.H. designed and carried out the experiments and data analysis. C.Q. performed the tiny-sci-RNA-seq bioinformatic analysis. J.D.J. performed the library preparation for the inDrop scRNA-seq and bioinformatics analysis. H.G. and M.T. performed and analysed the sequential smFISH. B.K.M. performed the library preparation for tiny-sci-RNA-seq. D.-Y.C. collected rat serum. A.A.-C. and J.H.H. provided the gas mixer and pressurising chamber for the last day of ETiX embryoid culture. M.E. supervised the sequential smFISH performed by H.G. and M.T. F.H. supervised the scRNA-seq analysis performed by J.D.J. J.S. supervised the tiny-sci-RNA-seq analysis performed by B.K.M. and C.Q. M.Z.-G., G.A., C.E.H. and D.M.G. wrote the manuscript. M.Z.-G. conceived, planned and supervised the study. Data availability. All unique and stable reagents generated in this study are available from the corresponding author with a completed Materials Transfer Agreement. Raw single-cell sequencing data generated by this work have been deposited in the NCBI Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/) and are accessible through the following accession numbers: the inDrops scRNA-seq dataset is available at GSE189425; the tiny-sci-RNA-seq dataset is available at GSE209792. Source data are provided with this paper. Code availability. The code used to analyse the inDrops scRNA-seq data is available at https://github.com/fhlab/scRNAseq_inducedETX The code used to analyse the tiny-sci-RNA-seq data is available at https://github.com/ChengxiangQiu/ETiX_Amadei. Competing interests. J.H.H. is a founder and chief scientific advisor to RenewalBio Ltd. M.Z.-G., G.A. and C.E.H. are applicants and inventors on a patent filed jointly on 5 May 2022 by Caltech and the University of Cambridge pertaining to and covering 'Generation of Synthetic Embryos from Multiple Stem Cell Types' under CIT file no.: CIT-8826-P and serial number: 63/344,251. The other authors declare no competing interests. Peer review information. Nature thanks Segiu Pasca, Manu Setty and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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