Clevers, H. The intestinal crypt, a prototype stem cell compartment. Cell 154, 274284 (2013).

Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 10031007 (2007).

Shyer, A. E., Huycke, T. R., Lee, C., Mahadevan, L. & Tabin, C. J. Bending gradients: how the intestinal stem cell gets its home. Cell 161, 569580 (2015).

Nigmatullina, L. et al. Id2 controls specification of Lgr5+ intestinal stem cell progenitors during gut development. EMBO J. 36, 869885 (2017).

Tetteh, P. W. et al. Replacement of lost Lgr5-positive stem cells through plasticity of their enterocyte-lineage daughters. Cell Stem Cell 18, 203213 (2016).

van Es, J. H. et al. Dll1+ secretory progenitor cells revert to stem cells upon crypt damage. Nat. Cell Biol. 14, 10991104 (2012).

Buczacki, S. J. et al. Intestinal label-retaining cells are secretory precursors expressing Lgr5. Nature 495, 6569 (2013).

Yui, S. et al. YAP/TAZ-dependent reprogramming of colonic epithelium links ECM remodeling to tissue regeneration. Cell Stem Cell 22, 3549 (2018).

Nusse, Y. M. et al. Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche. Nature 559, 109113 (2018).

Guiu, J. & Jensen, K. B. From definitive endoderm to gut-a process of growth and maturation. Stem Cells Dev. 24, 19721983 (2015).

Sumigray, K. D., Terwilliger, M. & Lechler, T. Morphogenesis and compartmentalization of the intestinal crypt. Dev. Cell 45, 183197 (2018).

Mustata, R. C. et al. Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium. Cell Reports 5, 421432 (2013).

Moor, A. E. et al. Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis. Cell 175, 11561167 (2018).

Merlos-Suarez, A. et al. The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse. Cell Stem Cell 8, 511524 (2011).

Shyer, A. E. et al. Villification: how the gut gets its villi. Science 342, 212218 (2013).

Walton, K. D. et al. Hedgehog-responsive mesenchymal clusters direct patterning and emergence of intestinal villi. Proc. Natl Acad. Sci. USA 109, 1581715822 (2012).

Itzkovitz, S., Blat, I. C., Jacks, T., Clevers, H. & van Oudenaarden, A. Optimality in the development of intestinal crypts. Cell 148, 608619 (2012).

Sato, T. et al. Single Lgr5 stem cells build cryptvillus structures in vitro without a mesenchymal niche. Nature 459, 262265 (2009).

Fordham, R. P. et al. Transplantation of expanded fetal intestinal progenitors contributes to colon regeneration after injury. Cell Stem Cell 13, 734744 (2013).

Yui, S. et al. Functional engraftment of colon epithelium expanded in vitro from a single adult Lgr5+ stem cell. Nat. Med. 18, 618623 (2012).

Ritsma, L. et al. Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging. Nature 507, 362365 (2014).

Tian, H. et al. A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable. Nature 478, 255259 (2011).

Chan, C. J., Heisenberg, C. P. & Hiiragi, T. Coordination of morphogenesis and cell-fate specification in development. Curr. Biol. 27, R1024R1035 (2017).

Hannan, N. R. et al. Generation of multipotent foregut stem cells from human pluripotent stem cells. Stem Cell Reports 1, 293306 (2013).

Spence, J. R. et al. Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature 470, 105109 (2011).

Watson, C. L. et al. An in vivo model of human small intestine using pluripotent stem cells. Nat. Med. 20, 13101314 (2014).

Sun, X. et al. Directed differentiation of human embryonic stem cells into thymic epithelial progenitor-like cells reconstitutes the thymic microenvironment in vivo. Cell Stem Cell 13, 230236 (2013).

McCracken, K. W. et al. Modelling human development and disease in pluripotent stem-cell-derived gastric organoids. Nature 516, 400404 (2014).

Kroon, E. et al. Pancreatic endoderm derived from human embryonic stem cells generates glucose-responsive insulin-secreting cells in vivo. Nat. Biotechnol. 26, 443452 (2008).

Muzumdar, M. D., Tasic, B., Miyamichi, K., Li, L. & Luo, L. A global double-fluorescent Cre reporter mouse. Genesis 45, 593605 (2007).

Means, A. L., Xu, Y., Zhao, A., Ray, K. C. & Gu, G. A CK19CreERT knockin mouse line allows for conditional DNA recombination in epithelial cells in multiple endodermal organs. Genesis 46, 318323 (2008).

Snippert, H. J. et al. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell 143, 134144 (2010).

el Marjou, F. et al. Tissue-specific and inducible Cre-mediated recombination in the gut epithelium. Genesis 39, 186193 (2004).

Madisen, L. et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 13, 133140 (2010).

Walton, K. D. & Kolterud, A. Mouse fetal whole intestine culture system for ex vivo manipulation of signaling pathways and three-dimensional live imaging of villus development. J. Vis. Exp. 91, e51817 (2014).

Zheng, G. X. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).

Fan, J. et al. Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nat. Methods 13, 241244 (2016).

Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411420 (2018).

Read the original:
Tracing the origin of adult intestinal stem cells | Nature