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Intestinal label-retaining cells are secretory precursors expressing Lgr5


The rapid cell turnover of the intestinal epithelium is achieved from small numbers of stem cells located in the base of glandular crypts. These stem cells have been variously described as rapidly cycling or quiescent. A functional arrangement of stem cells that reconciles both of these behaviours has so far been difficult to obtain. Alternative explanations for quiescent cells have been that they act as a parallel or reserve population that replace rapidly cycling stem cells periodically or after injury; their exact nature remains unknown. Here we show mouse intestinal quiescent cells to be precursors that are committed to mature into differentiated secretory cells of the Paneth and enteroendocrine lineage. However, crucially we find that after intestinal injury they are capable of extensive proliferation and can give rise to clones comprising the main epithelial cell types. Thus, quiescent cells can be recalled to the stem-cell state. These findings establish quiescent cells as an effective clonogenic reserve and provide a motivation for investigating their role in pathologies such as colorectal cancers and intestinal inflammation.

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Figure 1: Identification and isolation of YFP–LRCs.
Figure 2: YFP–LRCs are a discrete Lgr5-expressing subpopulation.
Figure 3: Acquisition of Paneth and enteroendocrine cell characteristics from YFP–LRCs.
Figure 4: LRCs only demonstrate clonogenicity after injury in vivo.

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Gene Expression Omnibus

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Data were deposited to the GEO database under accession number GSE43772.


  1. Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007 (2007)

    Article  CAS  ADS  Google Scholar 

  2. Roth, S. et al. Paneth cells in intestinal homeostasis and tissue injury. PLoS ONE 7, e38965 (2012)

    Article  CAS  ADS  Google Scholar 

  3. Powell, A. E. et al. The Pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor. Cell 149, 146–158 (2012)

    Article  CAS  Google Scholar 

  4. Sangiorgi, E. & Capecchi, M. R. Bmi1 is expressed in vivo in intestinal stem cells. Nature Genet. 40, 915–920 (2008)

    Article  CAS  Google Scholar 

  5. Montgomery, R. K. et al. Mouse telomerase reverse transcriptase (mTert) expression marks slowly cycling intestinal stem cells. Proc. Natl Acad. Sci. USA 108, 179–184 (2011)

    Article  CAS  ADS  Google Scholar 

  6. Takeda, N. et al. Interconversion between intestinal stem cell populations in distinct niches. Science 334, 1420–1424 (2011)

    Article  CAS  ADS  Google Scholar 

  7. Wong, V. W. et al. Lrig1 controls intestinal stem-cell homeostasis by negative regulation of ErbB signalling. Nature Cell Biol. 14, 401–408 (2012)

    Article  CAS  Google Scholar 

  8. Lopez-Garcia, C., Klein, A. M., Simons, B. D. & Winton, D. J. Intestinal stem cell replacement follows a pattern of neutral drift. Science 330, 822–825 (2010)

    Article  CAS  ADS  Google Scholar 

  9. Snippert, H. J. et al. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell 143, 134–144 (2010)

    Article  CAS  Google Scholar 

  10. Li, L. & Clevers, H. Coexistence of quiescent and active adult stem cells in mammals. Science 327, 542–545 (2010)

    Article  CAS  ADS  Google Scholar 

  11. Tian, H. et al. A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable. Nature 478, 255–259 (2011)

    Article  CAS  ADS  Google Scholar 

  12. Potten, C. S., Hume, W. J., Reid, P. & Cairns, J. The segregation of DNA in epithelial stem cells. Cell 15, 899–906 (1978)

    Article  CAS  Google Scholar 

  13. Potten, C. S., Owen, G. & Booth, D. Intestinal stem cells protect their genome by selective segregation of template DNA strands. J. Cell Sci. 115, 2381–2388 (2002)

    CAS  PubMed  Google Scholar 

  14. Demidov, O. N. et al. Wip1 phosphatase regulates p53-dependent apoptosis of stem cells and tumorigenesis in the mouse intestine. Cell Stem Cell 1, 180–190 (2007)

    Article  CAS  Google Scholar 

  15. He, X. C. et al. BMP signaling inhibits intestinal stem cell self-renewal through suppression of Wnt-β-catenin signaling. Nature Genet. 36, 1117–1121 (2004)

    Article  CAS  Google Scholar 

  16. He, X. C. et al. PTEN-deficient intestinal stem cells initiate intestinal polyposis. Nature Genet. 39, 189–198 (2007)

    Article  CAS  Google Scholar 

  17. Muñoz, J. et al. The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers. EMBO J. 31, 3079–3091 (2012)

    Article  Google Scholar 

  18. Ireland, H., Houghton, C., Howard, L. & Winton, D. J. Cellular inheritance of a Cre-activated reporter gene to determine Paneth cell longevity in the murine small intestine. Dev. Dyn. 233, 1332–1336 (2005)

    Article  CAS  Google Scholar 

  19. Foudi, A. et al. Analysis of histone 2B-GFP retention reveals slowly cycling hematopoietic stem cells. Nature Biotechnol. 27, 84–90 (2009)

    Article  CAS  Google Scholar 

  20. Sato, T. et al. Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts. Nature 469, 415–418 (2011)

    Article  CAS  ADS  Google Scholar 

  21. Cheng, H. & Leblond, C. P. Origin, differentiation and renewal of the four main epithelial cell types in the mouse small intestine. V. Unitarian Theory of the origin of the four epithelial cell types. Am. J. Anat. 141, 537–561 (1974)

    Article  CAS  Google Scholar 

  22. Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009)

    Article  CAS  ADS  Google Scholar 

  23. Jullien, N., Sampieri, F., Enjalbert, A. & Herman, J. P. Regulation of Cre recombinase by ligand-induced complementation of inactive fragments. Nucleic Acids Res. 31, e131 (2003)

    Article  Google Scholar 

  24. van Es, J. H. et al. Dll1+ secretory progenitor cells revert to stem cells upon crypt damage. Nature Cell Biol. 14, 1099–1104 (2012)

    Article  CAS  Google Scholar 

  25. Lewis, A. et al. Severe polyposis in Apc(1322T) mice is associated with submaximal Wnt signalling and increased expression of the stem cell marker Lgr5. Gut 59, 1680–1686 (2010)

    Article  CAS  Google Scholar 

  26. Campbell, S. J. et al. Regulation of the CYP1A1 promoter in transgenic mice: an exquisitely sensitive on-off system for cell specific gene regulation. J. Cell Sci. 109, 2619–2625 (1996)

    CAS  PubMed  Google Scholar 

  27. Vooijs, M., Jonkers, J. & Berns, A. A highly efficient ligand-regulated Cre recombinase mouse line shows that LoxP recombination is position dependent. EMBO Rep. 2, 292–297 (2001)

    Article  CAS  Google Scholar 

  28. McCutcheon, S. C. et al. Characterization of a heat resistant β-glucosidase as a new reporter in cells and mice. BMC Biol. 8, 89 (2010)

    Article  Google Scholar 

  29. Gracz, A. D., Ramalingam, S. & Magness, S. T. Sox9 expression marks a subset of CD24-expressing small intestine epithelial stem cells that form organoids in vitro. Am. J. Physiol. Gastrointest. Liver Physiol. 298, G590–G600 (2010)

    Article  CAS  Google Scholar 

  30. Potten, C. S. & Loeffler, M. Stem cells: attributes, cycles, spirals, pitfalls and uncertainties. Lessons for and from the crypt. Development 110, 1001–1020 (1990)

    CAS  PubMed  Google Scholar 

  31. Bjerknes, M. & Cheng, H. Methods for the isolation of intact epithelium from the mouse intestine. Anat. Rec. 199, 565–574 (1981)

    Article  CAS  Google Scholar 

  32. Irizarry, R. A. et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15 (2003)

    Article  Google Scholar 

  33. Pruitt, K. D., Tatusova, T., Klimke, W. & Maglott, D. R. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res. 37, D32–D36 (2009)

    Article  CAS  Google Scholar 

  34. Lockstone, H. E. Exon array data analysis using Affymetrix power tools and R statistical software. Brief. Bioinform. 12, 634–644 (2011)

    Article  CAS  Google Scholar 

  35. R Development Core Team. R: A Language and Environment for Statistical Computing (2009)

  36. Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004)

    Article  Google Scholar 

  37. Smyth, G. K. in Bioinformatics and Computational Biology Solutions using R and Bioconductor Solutions using R and Bioconductor (eds Carey, V., Gentleman, R., Dudoit, S., Huber, W. & Izzarry, R.) 397–420 (Springer, 2005)

    Book  Google Scholar 

  38. Jensen, K. B. & Watt, F. M. Single-cell expression profiling of human epidermal stem and transit-amplifying cells: Lrig1 is a regulator of stem cell quiescence. Proc. Natl Acad. Sci. USA 103, 11958–11963 (2006)

    Article  CAS  ADS  Google Scholar 

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This research was supported by Cancer Research UK (S.J.A.B., H.I.Z., A.M.N., R.R., R.K. and D.J.W.). L.V. was supported by a KWF fellowship. We thank D. Tan for providing the single-cell RNA amplification protocol. We also thank M. de la Roche, R. von Furstenberg and S. Henning for advice with the in vitro culture work. We acknowledge the following core facilities at CRUK/CRI: The Transgenic Laboratory, Biological Resource Unit, Flow Cytometry, Histopathology, Microscopy, Genomics and Bioinformatics and the CRUK Paterson Institute Microarray Facility. We thank R. J. Davies, A. Klein and A. Ibrahim for manuscript discussions.

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Authors and Affiliations



S.J.A.B. designed and performed experiments and wrote the paper. H.I.Z. designed and developed the H2B–YFP model and performed experiments. R.R. performed the bioinformatic analysis. A.M.N. and L.V. performed experiments. R.K. designed experiments and performed bioinformatic analysis. D.J.W. designed experiments, developed the diCreAB model and wrote the paper.

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Correspondence to Douglas J. Winton.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-6. (PDF 2399 kb)

H2B-YFP Paneth cells are non-responsive to βNF induction

Confocal reconstruction video of an isolated crypt immediately following βNF treatment, showing all cells other than Paneth cells express YFP. Yellow=YFP. Red=UEA. (MOV 4370 kb)

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Buczacki, S., Zecchini, H., Nicholson, A. et al. Intestinal label-retaining cells are secretory precursors expressing Lgr5. Nature 495, 65–69 (2013).

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