Abstract
Gastrulation, a critical developmental stage involving germ layer specification and axes formation, is a major point of failure in human development, contributing to pregnancy loss and congenital malformations. However, due to ethical constraints and anatomical differences in animal models, the failure modes underlying human gastrulation remain poorly understood. To elucidate these failure modes, we introduce FATE-MAP (Failure Analysis and Trajectory Evaluation via Mechanistic-AI Prediction), an integrated platform that combines high-throughput perturbations of human 2D gastruloids with quantitative phenotypic mapping, predictive deep learning, and mechanistic morphogen modeling. Analyzing over 2000 drug-treated human 2D gastruloids, we mapped a phenotypic morphospace that separates canonical patterning, in which primitive-streak fates are correctly specified and radially organized, from failure modes, defined as departures from this organization and marked by a loss of a required fate and/or radial symmetry. To predict and interpret patterning outcomes, FATE-MAP combines a transformer linking chemical structure to phenotype with PDE simulations of morphogen transport and cell fate specification, and projects both outputs onto the experimentally defined morphospace. Applying this framework, we flagged two clinical molecules as potential teratogens and identified two parameters, cell density and SOX2 stability, that form orthogonal morphospace axes along which canonically patterned gastruloids systematically vary. FATE-MAP thus provides a roadmap for decoding human developmental trajectories and accelerating safe therapeutic discovery.
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Data availability
The raw and processed gastruloid images and corresponding morphospace data (radial intensity profiles and cluster assignments) used in all analyses are publicly available at (https://max-wilson.mcdb.ucsb.edu/research/gastruloid-morphospace and https://github.com/MZW-Lab/gastruloid_morphospace). These datasets include the binned radial fluorescence intensity profiles for each colony and constitute the complete dataset used to generate the results reported in this study. Additional phenotype categorizations are provided in the Supplementary Information/Source Data file.
Code availability
All code generated during this study has been deposited at the Wilson Github repository (https://github.com/MZW-Lab/gastruloid_morphospace).
References
Roberts, C. J. & Lowe, C. R. Where have all the conceptions gone?. Lancet 305, 498–499 (1975).
Ghimire, S., Mantziou, V., Moris, N. & Arias, A. Martinez. human gastrulation: the embryo and its models. Dev. Biol. 474, 100–108 (2021).
Macklon, N. S., Geraedts, J. P. M. & Fauser, B. C. J. M. Conception to ongoing pregnancy: the ‘black box’of early pregnancy loss. Hum. Reprod. update 8, 333–343 (2002).
Chard, T. Frequency of implantation and early pregnancy loss in natural cycles. Bailliere’s. Clin. Obstet. Gynaecol. 5, 179–189 (1991).
Gerri, C. et al. Human embryogenesis: a comparative perspective. Annu. Rev. Cell Dev. Biol. 36, 411–440 (2020).
Pereira, D. et al. Modelling human embryogenesis: embryo-like structures spark ethical and policy debate. Hum. Reprod. Update 26, 779–798 (2020).
Ferrer-Vaquer, A. & Hadjantonakis, A.-K. Birth defects associated with perturbations in preimplantation, gastrulation, and axis extension: from conjoined twinning to caudal dysgenesis. Wiley Interdiscip. Rev.: Dev. Biol. 2, 427–442 (2013).
Herion, N. J., Salbaum, J. M. & Kappen, C. Traffic jam in the primitive streak: the role of defective mesoderm migration in birth defects. Birth Defects Res. Part A: Clin. Mol. Teratol. 100, 608–622 (2014).
Curtin, S. C., Tejada-Vera, B. & Bastian, B. A. Deaths: Leading causes for 2021. (Hyattsville, MD, 2024).
Wallingford, J. B. We are all developmental biologists. Dev. Cell 50, 132–137 (2019).
Kochanek, K. D., Murphy, S. L., Xu, J. & Arias, E. Mortality in the United States, 2022. (Hyattsville, MD, 2024).
Feldkamp, M. L. et al. Etiology and clinical presentation of birth defects: population based study. BMJ 357, j2249 (2017).
Toufaily, M. H., Westgate, M.-N., Lin, A. E. & Holmes, L. B. Causes of congenital malformations. Birth Defects Res. 110, 87–91 (2018).
Brent, R. L. Drug testing in animals for teratogenic effects: thalidomide in the pregnant rat. J. Pediatr. 64, 762–770 (1964).
Asatsuma-Okumura, T., Ito, T. & Handa, H. Molecular mechanisms of the teratogenic effects of thalidomide. Pharmaceuticals 13, 95 (2020).
Budd, G. E. Morphospace. Curr. Biol. 31, R1181–R1185 (2021).
Alberch, P. The logic of monsters: evidence for internal constraint in development and evolution. Geobios 22, 21–57 (1989).
Fu, J., Warmflash, A. & Lutolf, M. P. Stem-cell-based embryo models for fundamental research and translation. Nat. Mater. 20, 132–144 (2021).
Oldak, B. et al. Complete human day 14 post-implantation embryo models from naive ES cells. Nature 622, 562–573 (2023).
Weatherbee, B. A. T. et al. Pluripotent stem cell-derived model of the post-implantation human embryo. Nature 622, 584–593 (2023).
Liu, L. et al. Modeling post-implantation stages of human development into early organogenesis with stem-cell-derived peri-gastruloids. Cell 186, 3776–3792 (2023).
Shao, Y. et al. A pluripotent stem cell-based model for post-implantation human amniotic sac development. Nat. Commun. 8, 208 (2017).
Kagawa, H. et al. Scholte op Reimer, Yvonne, Castel, Gaël, Bruneau, Alexandre & Maenhoudt, Nina. Human blastoids model blastocyst development and implantation. Nature 601, 600–605 (2022).
Moris, N. et al. An in vitro model of early anteroposterior organization during human development. Nature 582, 410–415 (2020).
Sanaki-Matsumiya, M. et al. Periodic formation of epithelial somites from human pluripotent stem cells. Nat. Commun. 13, 2325 (2022).
Warmflash, A. et al. A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nat. methods 11, 847–854 (2014).
Karzbrun, E. et al. Human neural tube morphogenesis in vitro by geometric constraints. Nature 599, 268–272 (2021).
Deglincerti, A. et al. Self-organization of human embryonic stem cells on micropatterns. Nat. Protoc. 11, 2223–2232 (2016).
Minn, K. T. et al. High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human ESC gastruloid cultures. Elife 9, e59445 (2020).
Stephens, G. J., Johnson-Kerner, B., Bialek, W. & Ryu, W. S. Dimensionality and dynamics in the behavior of C. elegans. PLoS Comput. Biol. 4, e1000028 (2008).
Berman, G. J., Choi, D. M., Bialek, W. & Shaevitz, J. W. Mapping the stereotyped behaviour of freely moving fruit flies. J. R. Soc. Interface 11, 20140672 (2014).
Chithrananda, S., Grand, G. & Ramsundar, B. ChemBERTa: large-scale self-supervised pretraining for molecular property prediction. arXiv preprint arXiv:2010.09885 (2020).
Nau, H. Teratogenicity of isotretinoin revisited: species variation and the role of all-trans-retinoic acid. J. Am. Acad. Dermatol. 45, S183–S187 (2001).
Pignatello, M. A., Kauffman, F. C. & Levin, A. A. Multiple factors contribute to the toxicity of the aromatic retinoid, TTNPB (Ro 13-7410): binding affinities and disposition. Toxicol. Appl. Pharmacol. 142, 319–327 (1997).
Takamura, Y. et al. Teratogenicity and Fetal-Transfer Assessment of the Retinoid X Receptor Agonist Bexarotene. ACS Pharmacol. Transl. Sci. 5, 811–818 (2022).
Jaklin, M. et al. Optimization of the TeraTox assay for preclinical teratogenicity assessment. Toxicol. Sci. 188, 17–33 (2022).
Swiatek, P. J. et al. Notch1 is essential for postimplantation development in mice. Genes Dev. 8, 707–719 (1994).
Yao, Y. et al. Extracellular signal-regulated kinase 2 is necessary for mesoderm differentiation. Proc. Natl. Acad. Sci. 100, 12759–12764 (2003).
Jarque, S. et al. Morphometric analysis of developing zebrafish embryos allows predicting teratogenicity modes of action in higher vertebrates. Reprod. Toxicol. 96, 337–348 (2020).
Etoc, F. et al. A balance between secreted inhibitors and edge sensing controls gastruloid self-organization. Dev.Cell 39, 302–315 (2016).
Smith, Q. et al. Cytoskeletal tension regulates mesodermal spatial organization and subsequent vascular fate. Proc. Natl. Acad. Sci. 115, 8167–8172 (2018).
Blin, G. et al. Geometrical confinement controls the asymmetric patterning of brachyury in cultures of pluripotent cells. Development 145, dev166025 (2018).
Teague, S. et al. Time-integrated BMP signaling determines fate in a stem cell model for early human development. Nat. Commun. 15, 1471 (2024).
Heemskerk, I. et al. Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells. Elife 8, e40526 (2019).
Nemashkalo, A., Ruzo, A., Heemskerk, I. & Warmflash, A. Morphogen and community effects determine cell fates in response to BMP4 signaling in human embryonic stem cells. Development 144, 3042–3053 (2017).
Camacho-Aguilar, E. et al. Combinatorial interpretation of BMP and WNT controls the decision between primitive streak and extraembryonic fates. Cell Syst. 15, 445–461.e444 (2024).
Chhabra, S. et al. Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids. PLoS Biol. 17, e3000498 (2019).
Li, Y. et al. Volumetric compression induces intracellular crowding to control intestinal organoid growth via Wnt/β-catenin signaling. cell stem cell 28, e67 (2021).
Lach, R. S. et al. Nucleation of the destruction complex on the centrosome accelerates degradation of β-catenin and regulates Wnt signal transmission. Proc. Natl. Acad. Sci. 119, e2204688119 (2022).
Sayed, S. et al. Isoxazole 9 (ISX9), a small molecule targeting Axin, activates Wnt/β-catenin signalling and promotes hair regrowth. Br. J. Pharmacol. 180, 1748–1765 (2023).
Xiong, Y. et al. Longdaysin inhibits Wnt/β-catenin signaling and exhibits antitumor activity against breast cancer. OncoTargets and Therapy 12, 993–1005 (2019).
Johnson, E. M. & Christian, M. S. When is a teratology study not an evaluation of teratogenicity? J. Am. Coll. Toxicol. 3, 431–434 (1984).
Li, A. S. W. & Marikawa, Y. An in vitro gastrulation model recapitulates the morphogenetic impact of pharmacological inhibitors of developmental signaling pathways. Mol. Reprod. Dev. 82, 1015–1036 (2015).
Xing, J., Toh, Y.-C., Xu, S. & Yu, H. A method for human teratogen detection by geometrically confined cell differentiation and migration. Sci. Rep. 5, 10038 (2015).
Xing, J. et al. In vitro micropatterned human pluripotent stem cell test (µP-HPST) for morphometric-based teratogen screening. Sci. Rep. 7, 8491 (2017).
Esfahani, S. N. et al. Microengineered human amniotic ectoderm tissue array for high-content developmental phenotyping. Biomaterials 216, 119244 (2019).
Kameoka, S., Babiarz, J., Kolaja, K. & Chiao, E. A high-throughput screen for teratogens using human pluripotent stem cells. toxicological Sci. 137, 76–90 (2014).
Adam, M. P., P., Janine E. & Friedman, J. M. In American Journal of Medical Genetics Part C: Seminars in Medical Genetics. 175-182 (Wiley Online Library).
Sarayani, A. et al. Prenatal exposure to teratogenic medications in the era of Risk Evaluation and Mitigation Strategies. Am. J. Obstet. Gynecol. 227, 263.e261–263.e238 (2022).
Mihm, C. Substantial efforts needed to achieve greater progress on high-risk areas (GAO-19-157SP). Government Accountability Office (2019).
Knudsen, T. B. et al. Developmental toxicity testing for safety assessment: new approaches and technologies. Birth Defects Res. Part B: Dev. Reprod. Toxicol. 92, 413–420 (2011).
Martyn, I., Brivanlou, A. H. & Siggia, E. D. A wave of WNT signaling balanced by secreted inhibitors controls primitive streak formation in micropattern colonies of human embryonic stem cells. Development 146, dev172791 (2019).
Johnson, H. E. & Toettcher, J. E. Signaling dynamics control cell fate in the early Drosophila embryo. Dev. Cell 48, 361–370 (2019).
Muncie, J. M. et al. Mechanical tension promotes formation of gastrulation-like nodes and patterns mesoderm specification in human embryonic stem cells. Dev. Cell 55, 679–694.e611 (2020).
Power, M.-A. & Tam, P. P. L. Onset of gastrulation, morphogenesis and somitogenesis in mouse embryos displaying compensatory growth. Anat. Embryol. 187, 493–504 (1993).
Tam, P. P. L. Postimplantation development of mitomycin C-treated mouse blastocysts. Teratology 37, 205–212 (1988).
Lewis, N. E. & Rossant, J. Mechanism of size regulation in mouse embryo aggregates. Development 72, 169–181 (1982).
McDole, K. et al. In toto imaging and reconstruction of post-implantation mouse development at the single-cell level. Cell 175, 859–876.e833 (2018).
McNamara, H. M. et al. Recording morphogen signals reveals mechanisms underlying gastruloid symmetry breaking. Nat. cell Biol. 26, 1832–1844 (2024).
Fang, L. et al. A methylation-phosphorylation switch determines Sox2 stability and function in ESC maintenance or differentiation. Mol. cell 55, 537–551 (2014).
Huangfu, D. et al. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat. Biotechnol. 26, 795–797 (2008).
Maldonado, M. et al. ROCK inhibitor primes human induced pluripotent stem cells to selectively differentiate towards mesendodermal lineage via epithelial-mesenchymal transition-like modulation. Stem Cell Res. 17, 222–227 (2016).
Blassberg, R. et al. Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation. Nat. Cell Biol. 24, 633–644 (2022).
Villaronga-Luque, A. et al. Integrated molecular-phenotypic profiling reveals metabolic control of morphological variation in a stem-cell-based embryo model. Cell Stem Cell 32, 759–777.e713 (2025).
Kao, J. et al. Teratogenicity of valproic acid: in vivo and in vitro investigations. Teratog. Carcinog. Mutagen. 1, 367–382 (1981).
Guzzetta, A. et al. Hedgehog–FGF signaling axis patterns anterior mesoderm during gastrulation. Proc. Natl. Acad. Sci.USA 117, 15712–15723 (2020).
Jo, K. et al. Endogenous FGFs drive ERK-dependent cell fate patterning in 2D human gastruloids. Development 153, dev205459 (2026).
Jo, K. et al. Efficient differentiation of human primordial germ cells through geometric control reveals a key role for Nodal signaling. Elife 11, e72811 (2022).
Xia, C. et al. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl. Acad. Sci.USA. 116, 19490–19499 (2019).
Liu, L. et al. Nodal is a short-range morphogen with activity that spreads through a relay mechanism in human gastruloids. Nat. Commun. 13, 497 (2022).
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).
Acknowledgements
This study was supported by UCSB start-up funds. J.R. is supported by NICHD of the National Institutes of Health via a Ruth L. Kirschstein Postdoctoral Individual National Research Service Award (1F32HD114539-01). The authors acknowledge the use of the Microfluidics Laboratory within the California NanoSystems Institute, supported by the University of California, Santa Barbara and the University of California, Office of the President. Results related to the zebrafish teratogenicity assay were performed in collaboration with ZeClinics. The authors also thank Angela Pitenis and Dennis Clegg for their valuable feedback and discussions on experimental and figure design.
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Conceptualization, J.R., C.Q., D.H., and M.Z.W.; methodology, J.R., C.Q., D.H., N.B., G.D., and M.Z.W.; software and data analysis, J.R., C.Q., and M.Z.W.; modeling and simulations, J.R. and M.Z.W.; investigation, J.R., C.Q., D.H., N.B., G.D., J.D., and M.Z.W.; writing–original draft, J.R. and M.Z.W.; editing–final draft, J.R., F.W., J.J.C., and M.Z.W.; funding acquisition, J.R. and M.Z.W.
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F.W. and M.Z.W. are employees, shareholders, and board members of Integrated Biosciences Inc. J.J.C. is the founding Scientific Advisory Board chair of Integrated Biosciences. The remaining authors declare no competing interests.
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Rufo, J., Qiu, C., Han, D. et al. FATE-MAP predicts teratogenicity and human gastrulation failure modes by integrating deep learning and mechanistic modeling. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69596-6
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DOI: https://doi.org/10.1038/s41467-026-69596-6
