Turner, D. A. et al. Anteroposterior polarity and elongation in the absence of extra-embryonic tissues and of spatially localised signalling in gastruloids: mammalian embryonic organoids. Development 144, 3894–3906 (2017).
Veenvliet, J. V. et al. Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites. Science 370, eaba4937 (2020).
Moris, N. et al. An in vitro model of early anteroposterior organization during human development. Nature 582, 410–415 (2020).
Olmsted, Z. T. & Paluh, J. L. Co-development of central and peripheral neurons with trunk mesendoderm in human elongating multi-lineage organized gastruloids. Nat. Commun. 12, 3020 (2021).
Libby, A. R. G. et al. Axial elongation of caudalized human organoids mimics aspects of neural tube development. Development 148, dev198275 (2021).
Lee, J.-H. et al. Production of human spinal-cord organoids recapitulating neural-tube morphogenesis. Nat. Biomed. Eng. 6, 435–448 (2022).
Sanaki-Matsumiya, M. et al. Periodic formation of epithelial somites from human pluripotent stem cells. Nat. Commun. 13, 2325 (2022).
Yamanaka, Y. et al. Reconstituting human somitogenesis in vitro. Nature 614, 509–520 (2023).
Yaman, Y. I. & Ramanathan, S. Controlling human organoid symmetry breaking reveals signaling gradients drive segmentation clock waves. Cell 186, 513–527 (2023).
Anand, G. M. et al. Controlling organoid symmetry breaking uncovers an excitable system underlying human axial elongation. Cell 186, 497–512 (2023).
Corallo, D., Trapani, V. & Bonaldo, P. The notochord: structure and functions. Cell. Mol. Life Sci. 72, 2989–3008 (2015).
del Corral, R. D. & Storey, K. G. Opposing FGF and retinoid pathways: a signalling switch that controls differentiation and patterning onset in the extending vertebrate body axis. Bioessays 26, 857–869 (2004).
Stern, C. D. in Organization of the Early Vertebrate Embryo (eds Zagris, N. et al.) 139–147 (Springer, 1995).
Solovieva, T., Wilson, V. & Stern, C. D. A niche for axial stem cells – a cellular perspective in amniotes. Dev. Biol. 490, 13–21 (2022).
Charrier, J. B., Teillet, M. A., Lapointe, F. & Douarin, N. M. L. Defining subregions of Hensen’s node essential for caudalward movement, midline development and cell survival. Development 126, 4771–4783 (1999).
Cambray, N. & Wilson, V. Two distinct sources for a population of maturing axial progenitors. Development 134, 2829–2840 (2007).
Wilson, V., Olivera-Martinez, I. & Storey, K. G. Stem cells, signals and vertebrate body axis extension. Development 136, 1591–1604 (2009).
Williams, R. M., Lukoseviciute, M., Sauka-Spengler, T. & Bronner, M. E. Single-cell atlas of early chick development reveals gradual segregation of neural crest lineage from the neural plate border during neurulation. Elife 11, e74464 (2022).
Vermillion, K. L. et al. Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes. Dev. Biol. 439, 30–41 (2018).
Guillot, C., Djeffal, Y., Michaut, A., Rabe, B. & Pourquié, O. Dynamics of primitive streak regression controls the fate of neuromesodermal progenitors in the chicken embryo. Elife 10, e64819 (2021).
Trevers, K. E. et al. A gene regulatory network for neural induction. Elife 12, e73189 (2023).
Ataca, D. et al. The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche. Nat. Commun. 11, 1571 (2020).
Kitajima, S., Takagi, A., Inoue, T. & Saga, Y. MesP1 and MesP2 are essential for the development of cardiac mesoderm. Development 127, 3215–3226 (2000).
Stern, C. D. Initial patterning of the central nervous system: how many organizers? Nat. Rev. Neurosci. 2, 92–98 (2001).
Streit, A., Berliner, A. J., Papanayotou, C., Sirulnik, A. & Stern, C. D. Initiation of neural induction by FGF signalling before gastrulation. Nature 406, 74–78 (2000).
Wymeersch, F. J., Wilson, V. & Tsakiridis, A. Understanding axial progenitor biology in vivo and in vitro. Development 148, dev180612 (2021).
Albors, A. R., Halley, P. A. & Storey, K. G. Lineage tracing of axial progenitors using Nkx1-2CreERT2 mice defines their trunk and tail contributions. Development 145, dev164319 (2018).
de Lemos, L., Dias, A., Nóvoa, A. & Mallo, M. Epha1 is a cell-surface marker for the neuromesodermal competent population. Development 149, dev198812 (2022).
Gouti, M. et al. A gene regulatory network balances neural and mesoderm specification during vertebrate trunk development. Dev. Cell 41, 243–261 (2017).
Stein, S. & Kessel, M. A homeobox gene involved in node, notochord and neural plate formation of chick embryos. Mech. Dev. 49, 37–48 (1995).
Wilson, V. & Beddington, R. S. P. Cell fate and morphogenetic movement in the late mouse primitive streak. Mech. Dev. 55, 79–89 (1996).
Alto, L. T. & Terman, J. R. Semaphorin signaling, methods and protocols. Methods Mol. Biol. 1493, 1–25 (2016).
Chan, M. M. et al. Molecular recording of mammalian embryogenesis. Nature 570, 77–82 (2019).
Zhai, J. et al. Primate gastrulation and early organogenesis at single-cell resolution. Nature 612, 732–738 (2022).
Olivera-Martinez, I., Harada, H., Halley, P. A. & Storey, K. G. Loss of FGF-dependent mesoderm identity and rise of endogenous retinoid signalling determine cessation of body axis elongation. PLoS Biol. 10, e1001415 (2012).
Streit, A. & Stern, C. D. Mesoderm patterning and somite formation during node regression: differential effects of chordin and noggin. Mech. Dev. 85, 85–96 (1999).
Takemoto, T. Mechanism of cell fate choice between neural and mesodermal development during early embryogenesis. Congenit. Anom. 53, 61–66 (2013).
Onichtchouk, D. et al. Silencing of TGF-β signalling by the pseudoreceptor BAMBI. Nature 401, 480–485 (1999).
Solovieva, T., Lu, H.-C., Moverley, A., Plachta, N. & Stern, C. D. The embryonic node behaves as an instructive stem cell niche for axial elongation. Proc. Natl Acad. Sci. USA 119, e2108935119 (2022).
Verrier, L., Davidson, L., Gierliński, M., Dady, A. & Storey, K. G. Neural differentiation, selection and transcriptomic profiling of human neuromesodermal progenitor-like cells in vitro. Development 145, dev166215 (2018).
Gouti, M. et al. In vitro generation of neuromesodermal progenitors reveals distinct roles for Wnt signalling in the specification of spinal cord and paraxial mesoderm identity. PLoS Biol. 12, e1001937 (2014).
Lippmann, E. S. et al. Deterministic HOX patterning in human pluripotent stem cell-derived neuroectoderm. Stem Cell Rep. 4, 632–644 (2015).
Henrique, D., Abranches, E., Verrier, L. & Storey, K. G. Neuromesodermal progenitors and the making of the spinal cord. Development 142, 2864–2875 (2015).
Ring, D. B. et al. Selective glycogen synthase kinase 3 inhibitors potentiate insulin activation of glucose transport and utilization in vitro and in vivo. Diabetes 52, 588–595 (2003).
Warmflash, A., Sorre, B., Etoc, F., Siggia, E. D. & Brivanlou, A. H. A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nat. Methods 11, 847–854 (2014).
Haremaki, T. et al. Self-organizing neuruloids model developmental aspects of Huntington’s disease in the ectodermal compartment. Nat. Biotechnol. 37, 1198–1208 (2019).
Edri, S., Hayward, P., Baillie-Johnson, P., Steventon, B. & Arias, A. M. An epiblast stem cell derived multipotent progenitor population for axial extension. Development 146, dev.168187 (2019).
Edri, S., Hayward, P., Jawaid, W. & Arias, A. M. Neuromesodermal progenitors (NMPs): a comparative study between pluripotent stem cells and embryo derived populations. Development 146, dev.180190 (2019).
Piccolo, S., Sladitschek-Martens, H. L. & Cordenonsi, M. Mechanosignaling in vertebrate development. Dev. Biol. 488, 54–67 (2022).
Davis, J. R. & Tapon, N. Hippo signalling during development. Development 146, dev167106 (2019).
Zhao, B. et al. Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control. Genes Dev. 21, 2747–2761 (2007).
Morin-Kensicki, E. M. et al. Defects in yolk sac casculogenesis, chorioallantoic fusion, and embryonic axis elongation in mice with targeted disruption of Yap65. Mol. Cell. Biol. 26, 77–87 (2006).
Hubaud, A., Regev, I., Mahadevan, L. & Pourquié, O. Excitable dynamics and Yap-dependent mechanical cues drive the segmentation clock. Cell 171, 668–682 (2017).
Etoc, F. et al. A balance between secreted inhibitors and edge sensing controls gastruloid self-organization. Dev. Cell 39, 302–315 (2016).
Kastan, N. et al. Small-molecule inhibition of Lats kinases may promote Yap-dependent proliferation in postmitotic mammalian tissues. Nat. Commun. 12, 3100 (2021).
Pearson, J. D. et al. Binary pan-cancer classes with distinct vulnerabilities defined by pro- or anti-cancer YAP/TEAD activity. Cancer Cell 39, 1115–1134 (2021).
Yamaguchi, T. P., Takada, S., Yoshikawa, Y., Wu, N. & McMahon, A. P. T (Brachyury) is a direct target of Wnt3a during paraxial mesoderm specification. Genes Dev. 13, 3185–3190 (1999).
Azzolin, L. et al. YAP/TAZ incorporation in the β-catenin destruction complex orchestrates the Wnt response. Cell 158, 157–170 (2014).
Li, Q. et al. Lats1/2 sustain intestinal stem cells and Wnt activation through TEAD-dependent and independent transcription. Cell Stem Cell 26, 675–692 (2020).
Cadigan, K. M. & Waterman, M. L. TCF/LEFs and Wnt signaling in the nucleus. CSH Perspect. Biol. 4, a007906 (2012).
Schneider, A. et al. The homeobox gene it NKX3.2 is a target of left–right signalling and is expressed on opposite sides in chick and mouse embryos. Curr. Biol. 9, 911–914 (1999).
Dietrich, S., Schubert, F. R. & Gruss, P. Altered Pax gene expression in murine notochord mutants: the notochord is required to initiate and maintain ventral identity in the somite. Mech. Dev. 44, 189–207 (1993).
Rayon, T., Maizels, R. J., Barrington, C. & Briscoe, J. Single cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human specific features. Development 148, dev199711 (2021).
Schifferl, D. et al. A 37 kb region upstream of Brachyury comprising a notochord enhancer is essential for notochord and tail development. Development 148, dev200059 (2021).
Chiang, C. et al. Cyclopia and defective axial patterning in mice lacking Sonic hedgehog gene function. Nature 383, 407–413 (1996).
de Bree, K., de Bakker, B. S. & Oostra, R.-J. The development of the human notochord. PLoS ONE 13, e0205752 (2018).
Lehtonen, E., Stefanovic, V. & Saraga‐Babic, M. Changes in the expression of intermediate filaments and desmoplakins during development of human notochord. Differentiation 59, 43–49 (1995).
Babić, M. S. Relationship between notochord and the bursa pharyngea in early human development. Cell Differ. Dev. 32, 125–130 (1990).
Murakami, T., Wakamatsu, E., Tamahashi, N. & Takahashi, T. The functional significance of human notochord in the development of vertebral column. An electron microscopic study. Tohoku J. Exp. Med. 146, 321–336 (1985).
Xu, P.-F., Houssin, N., Ferri-Lagneau, K. F., Thisse, B. & Thisse, C. Construction of a vertebrate embryo from two opposing morphogen gradients. Science 344, 87–89 (2014).
Martyn, I., Brivanlou, A. H. & Siggia, E. D. A wave of WNT signalling balanced by secreted inhibitors controls primitive streak formation in micropattern colonies of human embryonic stem cells. Development 146, dev.172791 (2019).
Martyn, I., Siggia, E. D. & Brivanlou, A. H. Mapping cell migrations and fates in a gastruloid model to the human primitive streak. Development 146, dev179564 (2019).
Martyn, I., Kanno, T. Y., Ruzo, A., Siggia, E. D. & Brivanlou, A. H. Self-organization of a human organizer by combined Wnt and Nodal signalling. Nature 558, 132–135 (2018).
Stronati, E. et al. YAP1 regulates the self-organized fate patterning of hESC-derived gastruloids. Stem Cell Rep. 17, 211–220 (2022).
Sun, X. et al. Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers. Nucleic Acids Res. 48, 7182–7196 (2020).
Li, P. et al. Functional role of Mst1/Mst2 in embryonic stem cell differentiation. PLoS ONE 8, e79867 (2013).
Tonegawa, A. & Takahashi, Y. Somitogenesis controlled by Noggin. Dev. Biol. 202, 172–182 (1998).
Winzi, M. K., Hyttel, P., Dale, J. K. & Serup, P. Isolation and characterization of node/notochord-like cells from mouse embryonic stem cells. Stem Cells Dev. 20, 1817–1827 (2011).
Zhang, Y. et al. Directed differentiation of notochord-like and nucleus pulposus-like cells using human pluripotent stem cells. Cell Rep. 30, 2791–2806 (2020).
Petukhov, V. et al. dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. Genome Biol. 19, 78 (2018).
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
Wolock, S. L., Lopez, R. & Klein, A. M. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 8, 281–291 (2019).
Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).
Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).
Choi, H. M. T. et al. Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust. Development 145, dev165753 (2018).
Wu, Y., Kirillov, A., Massa, F., Lo, W.-Y. & Girshick, R. Detectron2. GitHub https://github.com/facebookresearch/detectron2 (2019).
Cai, Z. & Vasconcelos, N. Cascade R-CNN: Delving into high quality object detection. Preprint at https://doi.org/10.48550/arxiv.1712.00726 (2017).
Azioune, A., Storch, M., Bornens, M., Théry, M. & Piel, M. Simple and rapid process for single cell micro-patterning. Lab Chip 9, 1640–1642 (2009).
Shi, Y., Kirwan, P. & Livesey, F. J. Directed differentiation of human pluripotent stem cells to cerebral cortex neurons and neural networks. Nat. Protoc. 7, 1836–1846 (2012).
Kvon, E. Z. et al. Comprehensive in vivo interrogation reveals phenotypic impact of human enhancer variants. Cell 180, 1262–1271.e15 (2020).
Deerinck, T. J., Bushong, E., Thor, A. & Ellisman, M. NCMIR methods for 3D EM: a new protocol for preparation of biological specimens for serial block face scanning electron microscopy. 6–8 (2010).
Meechan, K. et al. Crosshair, semi-automated targeting for electron microscopy with a motorised ultramicrotome. eLife 11, e80899 (2022).
Cardona, A. et al. TrakEM2 software for neural circuit reconstruction. PLoS ONE 7, e38011 (2012).
Bogovic, J. A., Hanslovsky, P., Wong, A. & Saalfeld, S. Robust registration of calcium images by learned contrast synthesis. In Proc. 13th International Symposium on Biomedical Imaging 1123–1126 (IEEE, 2016).
Rito, T. PyTorch models for nucleus. Zenodo https://doi.org/10.1101/2023.02.27.530267 (2024).
Rito, T. PyTorch models for GastrUnet. Zenodo https://doi.org/10.5281/zenodo.12684780 (2024).
