Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007 (2007).
Tao, S. et al. Wnt activity and basal niche position sensitize intestinal stem and progenitor cells to DNA damage. EMBO J. 36, 2920–2921 (2017).
Nusse, Y. M. et al. Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche. Nature 562, 109–113 (2018).
Ayyaz, A. et al. Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell. Nature 569, 121–125 (2019).
de Sousa e Melo, F. & de Sauvage, F. J. Cellular plasticity in intestinal homeostasis and disease. Cell Stem Cell 24, 54–64 (2019).
Ohara, T. E., Colonna, M. & Stappenbeck, T. S. Adaptive differentiation promotes intestinal villus recovery. Dev. Cell 57, 166–179.e6 (2022).
Karo-Atar, D. et al. Helminth-induced reprogramming of the stem cell compartment inhibits type 2 immunity. J. Exp. Med. 219, e20212311 (2022).
Goldsmith, J. R. et al. TNFAIP8 controls murine intestinal stem cell homeostasis and regeneration by regulating microbiome-induced Akt signaling. Nat. Commun. 11, 2591 (2020).
Andersen, C. L. et al. Clusterin expression in normal mucosa and colorectal cancer. Mol. Cell Proteom. 6, 1039–1048 (2007).
Chen, X. et al. Clusterin as a biomarker in murine and human intestinal neoplasia. Proc. Natl Acad. Sci. USA 100, 9530–9535 (2003).
Yui, S. et al. YAP/TAZ-dependent reprogramming of colonic epithelium links ECM remodeling to tissue regeneration. Cell Stem Cell 22, 35–49.e7 (2018).
Morral, C. et al. p53 promotes revival stem cells in the regenerating intestine after severe radiation injury. Nat. Commun. 15, 3018 (2024).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).
Heuberger, J. et al. Shp2/MAPK signaling controls goblet/paneth cell fate decisions in the intestine. Proc. Natl Acad. Sci. USA 111, 3472–3477 (2014).
Wallaeys, C., Garcia‐Gonzalez, N. & Libert, C. Paneth cells as the cornerstones of intestinal and organismal health: a primer. EMBO Mol. Med. 15, e16427 (2023).
Treveil, A. et al. Regulatory network analysis of paneth cell and goblet cell enriched gut organoids using transcriptomics approaches. Mol. Omics 16, 39–58 (2020).
Kim, C. K. et al. Krüppel-like factor 5 regulates stemness, lineage specification, and regeneration of intestinal epithelial stem cells. Cell Mol. Gastroenterol. Hepatol. 9, 587–609 (2020).
van Es, J. H. et al. Wnt signalling induces maturation of paneth cells in intestinal crypts. Nat. Cell Biol. 7, 381–386 (2005).
Ishibashi, F. et al. Contribution of ATOH1+ cells to the homeostasis, repair, and tumorigenesis of the colonic epithelium. Stem Cell Rep. 10, 27–42 (2018).
Tomic, G. et al. Phospho-regulation of ATOH1 Is required for plasticity of secretory progenitors and tissue regeneration. Cell Stem Cell 23, 27–42 (2018).
Wester, R. A. et al. Retinoic acid signaling drives differentiation toward the absorptive lineage in colorectal cancer. iScience 24, 103444 (2021).
Hickey, J. W. et al. Organization of the human intestine at single-cell resolution. Nature 619, 572–584 (2023).
Lopez, R. et al. Deep generative modeling for single-cell transcriptomics. Nat. Methods 15, 1053–1058 (2018).
Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMG Genomics 19, 477 (2018).
Moor, A. E. et al. Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis. Cell 175, 1156–1167.e15 (2018).
Chen, L. et al. TGFB1 induces fetal reprogramming and enhances intestinal regeneration. Cell Stem Cell 30, 1520–1537.e8 (2023).
Hayashi, S., Lewis, P., Pevny, L. & McMahon, A. P. Efficient gene modulation in mouse epiblast using a Sox2Cre transgenic mouse strain. Mech. Dev. 119, 93–97 (2002).
Hayashi, H. et al. The MAD-related protein Smad7 associates with the TGFβ receptor and functions as an antagonist of TGFβ signaling. Cell 89, 1165–1173 (1997).
Tian, H. et al. A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable. Nature 478, 255–259 (2011).
Serra, D. et al. Self-organization and symmetry breaking in intestinal organoid development. Nature 569, 66–72 (2019).
Ko, T. C., Beauchamp, R. D., Townsend, C. M., Thompson, E. A. & Thompson, J. C. Transforming growth factor-β inhibits rat intestinal cell growth by regulating cell cycle specific gene expression. Am. J. Surg. 167, 14–20 (1994).
Yin, X. et al. Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny. Nat. Methods 11, 106–112 (2014).
El Marjou, F. et al. Tissue-specific and inducible Cre-mediated recombination in the gut epithelium. Genesis 39, 186–193 (2004).
Levéen, P. et al. Induced disruption of the transforming growth factor beta type II receptor gene in mice causes a lethal inflammatory disorder that is transplantable. Blood 100, 560–568 (2002).
Li, M. et al. Mothers against decapentaplegic-related protein 2 expression in avian granulosa cells is up-regulated by transforming growth factor β during ovarian follicular development. Endocrinology 138, 3659–3665 (1997).
Guillermin, O. et al. Wnt and Src signals converge on YAP‐TEAD to drive intestinal regeneration. EMBO J. 40, e105770 (2021).
Gregorieff, A., Liu, Y., Inanlou, M. R., Khomchuk, Y. & Wrana, J. L. Yap-dependent reprogramming of Lgr5+ stem cells drives intestinal regeneration and cancer. Nature 526, 715–718 (2015).
Barry, E. R. et al. Restriction of intestinal stem cell expansion and the regenerative response by YAP. Nature 493, 106–110 (2013).
Haber, A. L. et al. A single-cell survey of the small intestinal epithelium. Nature 551, 333–339 (2017).
Cai, J. et al. The Hippo signaling pathway restricts the oncogenic potential of an intestinal regeneration program. Genes Dev. 24, 2383–2388 (2010).
Sanman, L. E. et al. Transit-amplifying cells coordinate changes in intestinal epithelial cell-type composition. Dev. Cell 56, 356–365.e9 (2021).
Stuart, T., Srivastava, A., Madad, S., Lareau, C. A. & Satija, R. Single-cell chromatin state analysis with Signac. Nat. Methods 18, 1333–1341 (2021).
McGinnis, C. S., Murrow, L. M. & Gartner, Z. J. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 8, 329–337.e4 (2019).
Van den Berge, K. et al. Trajectory-based differential expression analysis for single-cell sequencing data. Nat. Commun. 11, 1201 (2020).
Sato, T. et al. Single Lgr5 stem cells build crypt–villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009).
Gregorieff, A. et al. Expression pattern of Wnt signaling components in the adult intestine. Gastroenterology 129, 626–638 (2005).
Caldwell, L. & Patel, S. Custom revSC analysis files for Fink et al. 2024, in Nature Cell Biology. Zenodo https://doi.org/10.5281/zenodo.13315436 (2024).
- SEO Powered Content & PR Distribution. Get Amplified Today.
- PlatoData.Network Vertical Generative Ai. Empower Yourself. Access Here.
- PlatoAiStream. Web3 Intelligence. Knowledge Amplified. Access Here.
- PlatoESG. Carbon, CleanTech, Energy, Environment, Solar, Waste Management. Access Here.
- PlatoHealth. Biotech and Clinical Trials Intelligence. Access Here.
- Source: https://www.nature.com/articles/s41556-024-01550-4