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Remodelling of the human embryo at implantation is indispensable for successful pregnancy. Yet it has remained mysterious because of the experimental hurdles that beset the study of this developmental phase. Here, we establish an in vitro system to culture human embryos through implantation stages in the absence of maternal tissues and reveal the key events of early human morphogenesis. These include segregation of the pluripotent embryonic and extra-embryonic lineages, and morphogenetic rearrangements leading to generation of a bilaminar disc, formation of a pro-amniotic cavity within the embryonic lineage, appearance of the prospective yolk sac, and trophoblast differentiation. Using human embryos and human pluripotent stem cells, we show that the reorganization of the embryonic lineage is mediated by cellular polarization leading to cavity formation. Together, our results indicate that the critical remodelling events at this stage of human development are embryo-autonomous, highlighting the remarkable and unanticipated self-organizing properties of human embryos.

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  • 17 May 2016

    In the version of this Technical Report originally published online, in Fig. 1d (which presents pilot in vitro culture experiments) it erroneously stated that 20% HCS was used in the IVC2 medium; it should have stated that 30% KSR was used. This error arose by a miscommunication between the postdoctoral fellow who contributed to the pilot in vitro culture experiments and prepared the media, and the postdoctoral fellow who performed the experiments. The composition of the media has been verified based on the laboratory notebooks that describe the media preparation. This error has been corrected in the labels and caption of Fig. 1d, in the description of the results in the main text, and in the Methods section, in all versions of the Technical Report.


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We are grateful to the patients donating their embryos, colleagues in the M.Z.-G. laboratory, C. Lee (Gurdon Institute), and embryologists at the CARE, Bourn Hall (K. Elder and P. Snell) and Kings College Guy’s Hospital IVF clinics for help and discussions. We thank P. Braude, D. Glover and C. Ogilvie for insightful discussion and I. Bedzhov for help in a pilot experiment. This work was supported by the Wellcome Trust grant to M.Z.-G. Work in the K.K.N. laboratory was supported by The Francis Crick Institute, which receives its core funding from Cancer Research UK, the Medical Research Council and the Wellcome Trust. M.N.S. was initially supported by a Ramon Areces Spanish Foundation Fellowship, and subsequently by an EMBO Postdoctoral Fellowship. S.V. was supported by a Post Doc Pool Grant from the Finnish Cultural Foundation. G.R. was supported by a Newton Fellowship.

Author information

Author notes

    • Marta N. Shahbazi
    • , Agnieszka Jedrusik
    •  & Sanna Vuoristo

    These authors contributed equally to this work.

    • Gaelle Recher

    Present address: Bioimaging and Optofluidics group, IOGS, CNRS & University of Bordeaux Rue Francois Mitterand, 33400 Talence, France.


  1. Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3DY, UK

    • Marta N. Shahbazi
    • , Agnieszka Jedrusik
    • , Sanna Vuoristo
    • , Gaelle Recher
    • , Anna Hupalowska
    •  & Magdalena Zernicka-Goetz
  2. Faculty of Life Sciences and Medicine, King’s College London, Women’s Health Academic Centre, Assisted Conception Unit, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK

    • Virginia Bolton
    • , Liani G. Devito
    • , Dusko Ilic
    •  & Yakoub Khalaf
  3. Human Embryo and Stem Cell Laboratory, Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK

    • Norah M. E. Fogarty
    •  & Kathy K. Niakan
  4. CARE Fertility Group, John Webster House, 6 Lawrence Drive, Nottingham Business Park, Nottingham NG8 6PZ, UK

    • Alison Campbell
    •  & Simon Fishel


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M.N.S., A.J. and S.V. carried out all experiments and data analyses. G.R. analysed microscopy data and generated 3D reconstructions. A.H. prepared illustrations and contributed experimentally. N.M.E.F. and K.K.N. helped with human embryo cultures and contributed experimentally, and L.G.D. helped with human embryo cultures. A.C., S.F., D.I., Y.K. and K.K.N. oversaw and provided human embryos for these studies. M.Z.-G. conceived the project and supervised the study. M.N.S. and M.Z.-G. wrote the manuscript with help from all of the authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Magdalena Zernicka-Goetz.

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  1. 1.

    Development of a day 5 human blastocyst in the in vitro culture system up to day 9–10.

    Related to Fig. 1. A day 5 human embryo was cultured in the in vitro culture system for approximately 100 h. Bright field images were taken every 30 min to record its development. Scale bar, 100 μm.

  2. 2.

    Development of a day 9 human blastocyst in the in vitro culture system up to day 12.

    Related to Fig. 1. A day 9 human embryo was cultured in the in vitro culture system for approximately 72 h. Bright field images were taken every 30 min to record its development. Scale bar, 100 μm.

  3. 3.

    3D reconstruction of embryonic lineages in a day 9–10 human embryo cultured in vitro.

    Related to Fig. 3. Nuclei are shown in blue, OCT4 in grey and GATA6/F-actin in green.

  4. 4.

    3D reconstruction of embryonic lineages in a day 10–11 human embryo cultured in vitro.

    Related to Fig. 3. Nuclei are shown in blue, OCT4 in grey and GATA6/F-actin in green.

  5. 5.

    3D reconstruction of the cellular and nuclear shape of representative trophectoderm cells at day 10–11.

    Related to Fig. 3. Nuclei are shown in magenta and membranes in green. Note that cells in close proximity to the epiblast have a single nucleus, whereas cells in the periphery of the embryo are multinucleated.

  6. 6.

    3D reconstruction of the pro-amniotic cavity at day 9–10.

    Related to Fig. 4. The nuclei of OCT4-expressing epiblast cells is shown in grey and the pro-amniotic cavity in red.

  7. 7.

    3D reconstruction of the cellular shape of representative OCT4-expressing epiblast cells at day 10–11.

    Related to Fig. 4. Epiblast cells in close proximity to GATA6-expressing hypoblast cells are shown in green (note the columnar shape characteristic of cells within the epiblast disc). Epiblast cells in close proximity to cytotrophoblast cells are shown in magenta (note the squamous shape characteristic of amniotic cells).

  8. 8.

    3D reconstruction of the prospective yolk sac at day 10–11.

    Related to Fig. 4. The nuclei of OCT4-expressing epiblast cells is shown in grey and the prospective yolk sac in blue.

  9. 9.

    3D reconstruction of the hypoblast derived cells and their position with respect to the prospective yolk sac at day 10–11.

    Related to Fig. 4. Nuclei of OCT4-expressing epiblast cells are shown in grey, GATA6/F-actin is shown in green and the prospective yolk sac in blue.

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