Willet, S. G. & Mills, J. C. Stomach organ and cell lineage differentiation: from embryogenesis to adult homeostasis. Cell. Mol. Gastroenterol. Hepatol. 2, 546–559 (2016).
Zorn, A. M. & Wells, J. M. Vertebrate endoderm development and organ formation. Annu. Rev. Cell Dev. Biol. 25, 221–251 (2009).
Kim, B. M., Buchner, G., Miletich, I., Sharpe, P. T. & Shivdasani, R. A. The stomach mesenchymal transcription factor Barx1 specifies gastric epithelial identity through inhibition of transient Wnt signaling. Dev. Cell 8, 611–622 (2005).
Listyorini, D. & Yasugi, S. Expression and function of Wnt5a in the development of the glandular stomach in the chicken embryo. Dev. Growth Differ. 48, 243–252 (2006).
Li, Y. et al. Sfrp5 coordinates foregut specification and morphogenesis by antagonizing both canonical and noncanonical Wnt11 signaling. Genes Dev. 22, 3050–3063 (2008).
Takamoto, N. et al. COUP-TFII is essential for radial and anteroposterior patterning of the stomach. Development 132, 2179–2189 (2005).
Kim, B. M. et al. Independent functions and mechanisms for homeobox gene Barx1 in patterning mouse stomach and spleen. Development 134, 3603–3613 (2007).
McCracken, K. W. et al. Modelling human development and disease in pluripotent stem-cell-derived gastric organoids. Nature 516, 400–404 (2014).
McCracken, K. W. et al. Wnt/beta-catenin promotes gastric fundus specification in mice and humans. Nature 541, 182–187 (2017).
Eicher, A. K. et al. Functional human gastrointestinal organoids can be engineered from three primary germ layers derived separately from pluripotent stem cells. Cell Stem Cell 29, 36–51 (2022).
Zhang, H. T. & Hiiragi, T. Symmetry breaking in the mammalian embryo. Annu. Rev. Cell Dev. Biol. 34, 405–426 (2018).
Shao, Y. & Fu, J. P. Engineering multiscale structural orders for high-fidelity embryoids and organoids. Cell Stem Cell 29, 722–743 (2022).
McGrath, P. S. & Wells, J. M. SnapShot: GI tract development. Cell 161, 176–176 (2015).
Mittal, R. et al. Organ-on-chip models: Implications in drug discovery and clinical applications. J. Cell. Physiol. 234, 8352–8380 (2019).
Hirami, Y. et al. Safety and stable survival of stem-cell-derived retinal organoid for 2 years in patients with retinitis pigmentosa. Cell Stem Cell 30, 1585–1596 (2023).
Karzbrun, E. et al. Human neural tube morphogenesis in vitro by geometric constraints. Nature 599, 268–272 (2021).
Libby, A. R. G. et al. Axial elongation of caudalized human organoids mimics aspects of neural tube development. Development 148, dev198275 (2021).
Takasato, M. et al. Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis. Nature 526, 564–568 (2015).
Taguchi, A. et al. Redefining the in vivo origin of metanephric nephron progenitors enables generation of complex kidney structures from pluripotent stem cells. Cell Stem Cell 14, 53–67 (2014).
Lin, F. et al. Mechanically enhanced biogenesis of gut spheroids with instability-driven morphomechanics. Nat. Commun. 14, 6016 (2023).
Reubinoff, B. E. et al. Neural progenitors from human embryonic stem cells. Nat. Biotechnol. 19, 1134–1140 (2001).
Wells, M. F. et al. Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages. Cell Stem Cell 30, 312–332 (2023).
Lee, G. et al. Isolation and directed differentiation of neural crest stem cells derived from human embryonic stem cells. Nat. Biotechnol. 25, 1468–1475 (2007).
Lignell, A., Kerosuo, L., Streichan, S. J., Cai, L. & Bronner, M. E. Identification of a neural crest stem cell niche by spatial genomic analysis. Nat. Commun. 8, 1830 (2017).
Zhao, L. Z., Song, W. L. & Chen, Y. G. Mesenchymal-epithelial interaction regulates gastrointestinal tract development in mouse embryos. Cell Rep. 40, 111053 (2022).
Yu, Q. et al. Charting human development using a multi-endodermal organ atlas and organoid models. Cell 184, 3281–3298 (2021).
Beumer, J. et al. High-resolution mRNA and secretome atlas of human enteroendocrine cells. Cell 181, 1291–1306 (2020).
Lan, X. et al. PCGF6 controls neuroectoderm specification of human pluripotent stem cells by activating SOX2 expression. Nat. Commun. 13, 4601 (2022).
Liu, D. D. et al. Purification and characterization of human neural stem and progenitor cells. Cell 186, 1179–1194 (2023).
Nagy, N. & Goldstein, A. M. Enteric nervous system development: a crest cell’s journey from neural tube to colon. Semin. Cell Dev. Biol. 66, 94–106 (2017).
Huang, M. et al. Generating trunk neural crest from human pluripotent stem cells. Sci. Rep. 6, 19727 (2016).
Mohlin, S. et al. Maintaining multipotent trunk neural crest stem cells as self-renewing crestospheres. Dev. Biol. 447, 137–146 (2019).
Elmentaite, R. et al. Cells of the human intestinal tract mapped across space and time. Nature 597, 250–255 (2021).
Zhai, J. L. et al. Primate gastrulation and early organogenesis at single-cell resolution. Nature 612, 732–738 (2022).
Gulati, G. S. et al. Single-cell transcriptional diversity is a hallmark of developmental potential. Science 367, 405–411 (2020).
Gao, S. et al. Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. Nat. Cell Biol. 20, 721–734 (2018).
Kim, J.-E. et al. Single cell and genetic analyses reveal conserved populations and signaling mechanisms of gastrointestinal stromal niches. Nat. Commun. 11, 334 (2020).
Shao, X. H. et al. MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. Nucleic Acids Res. 51, D1519–D1530 (2023).
Müller, M., Jabs, N., Lorke, D. E., Fritzsch, B. & Sander, M. Nkx6.1 controls migration and axon pathfinding of cranial branchio-motoneurons. Development 130, 5815–5826 (2003).
Gou, Y., Guo, J., Maulding, K. & Riley, B. B. sox2 and sox3 cooperate to regulate otic/epibranchial placode induction in zebrafish. Dev. Biol. 435, 84–95 (2018).
Wang, H. et al. The E3 ubiquitin ligase RNF220 maintains hindbrain Hox expression patterns through regulation of WDR5 stability. eLife 13, RP94657 (2024).
Zeng, B. et al. The single-cell and spatial transcriptional landscape of human gastrulation and brain. Cell Stem Cell 30, 851–866 (2023).
Xue, X. et al. A patterned human neural tube model using microfluidic gradients. Nature 628, 391–399 (2024).
Tyser, R. C. V. et al. Single-cell transcriptomic characterization of a gastrulating human embryo. Nature 600, 285–289 (2021).
Han, L. et al. Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nat. Commun. 11, 4158 (2020).
Smith, R. J. et al. Epigenetic control of cellular crosstalk defines gastrointestinal organ fate and function. Nat. Commun. 14, 497 (2023).
Zacchetti, G., Duboule, D. & Zakany, J. Hox gene function in vertebrate gut morphogenesis: the case of the caecum. Development 134, 3967–3973 (2007).
Pitera, J. E., Smith, V. V., Thorogood, P. & Milla, P. J. Coordinated expression of 3′ Hox genes during murine embryonal gut development: an enteric Hox code. Gastroenterology 117, 1339–1351 (1999).
Yahagi, N. et al. Position-specific expression of Hox genes along the gastrointestinal tract. Congenit. anom. 44, 18–26 (2004).
Jin, S. et al. Inference and analysis of cell-cell communication using CellChat. Nat. Commun. 12, 1088 (2021).
Grapin-Botton, A. & Melton, D. A. Endoderm development: from patterning to organogenesis. Trends Genet. 16, 124–130 (2000).
Nielsen, C., Murtaugh, L. C., Chyung, J. C., Lassar, A. & Roberts, D. J. Gizzard formation and the role of Bapx1. Dev. Biol. 231, 164–174 (2001).
Okamura, M. et al. COUP-TFII acts downstream of Wnt/β-catenin signal to silence PPARγ gene expression and repress adipogenesis. Proc. Natl Acad. Sci. USA 106, 5819–5824 (2009).
Fujimura, N., Taketo, M. M., Mori, M., Korinek, V. & Kozmik, Z. Spatial and temporal regulation of Wnt/β-catenin signaling is essential for development of the retinal pigment epithelium. Dev. Biol. 334, 31–45 (2009).
Broda, T. R., McCracken, K. W. & Wells, J. M. Generation of human antral and fundic gastric organoids from pluripotent stem cells. Nat. Protoc. 14, 28–50 (2019).
Zheng, Y. et al. Dorsal-ventral patterned neural cyst from human pluripotent stem cells in a neurogenic niche. Sci. Adv. 5, eaax5933 (2019).
Zhang, Q. et al. Hypoxia-responsive lncRNA AC115619 encodes and hepatocellular carcinoma progression. Cancer Res. 83, 2496–2512 (2023).
Renier, N. et al. iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging. Cell 159, 896–910 (2014).
Maynard, K. R. et al. dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues. Nucleic Acids Res. 48, e66 (2020).
Zhu, L. N. et al. Single-cell sequencing of peripheral mononuclear cells reveals distinct immune response landscapes of COVID-19 and influenza patients. Immunity 53, 685–696 (2020).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J. & Prins, P. Sambamba: fast processing of NGS alignment formats. Bioinformatics 31, 2032–2034 (2015).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
Qiu, X. et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979–982 (2017).
Wolf, F. A. et al. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol. 20, 59 (2019).
Farrell, J. A. et al. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science 360, eaar3131 (2018).
Wickam, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
van de Sande, B. et al. A scalable SCENIC workflow for single-cell gene regulatory network analysis. Nat. Protoc. 15, 2247–2276 (2020).
Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012).
Timme, N. M. & Lapish, C. A tutorial for information theory in neuroscience. eNeuro 5, ENEURO.0052-18.2018 (2018).
