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Identification of stem cells in small intestine and colon by marker gene Lgr5


The intestinal epithelium is the most rapidly self-renewing tissue in adult mammals. It is currently believed that four to six crypt stem cells reside at the +4 position immediately above the Paneth cells in the small intestine; colon stem cells remain undefined. Lgr5 (leucine-rich-repeat-containing G-protein-coupled receptor 5, also known as Gpr49) was selected from a panel of intestinal Wnt target genes for its restricted crypt expression. Here, using two knock-in alleles, we reveal exclusive expression of Lgr5 in cycling columnar cells at the crypt base. In addition, Lgr5 was expressed in rare cells in several other tissues. Using an inducible Cre knock-in allele and the Rosa26-lacZ reporter strain, lineage-tracing experiments were performed in adult mice. The Lgr5-positive crypt base columnar cell generated all epithelial lineages over a 60-day period, suggesting that it represents the stem cell of the small intestine and colon. The expression pattern of Lgr5 suggests that it marks stem cells in multiple adult tissues and cancers.

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Figure 1: Lgr5 is a Wnt target gene in a human colon cancer cell line and is expressed in mouse crypts.
Figure 2: Lgr5 expression in cycling CBC cells of the small intestine.
Figure 3: Restricted expression of an Lgr5-lacZ reporter gene in adult mice.
Figure 4: EGFP expression in an Lgr5-EGFP-IRES-creERT2 knock-in mouse faithfully reproduces the Lgr5-lacZ expression pattern in the intestinal tract.
Figure 5: Lineage tracing in the small intestine and colon.


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We thank R. Vries for preparing total RNA from isolated intestinal crypt and villus fractions and S. van den Brink for help with the embryonic stem cell work. We would like to acknowledge financial support from the following sources: Genmab B.V., Koninklijke Nederlandse Akademie van Wetenschappen (KNAW), Koningin Wilhelmina Fonds (KWF), Maag Lever en Darm Stichting (MLDS), European Molecular Biology Organization (EMBO), SenterNovem BSIK, Louis Jeantet Foundation and the European Union.

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Correspondence to Hans Clevers.

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Competing interests

H. Clevers is an inventor on several patents involving Wnt target genes, as is N. Barker.

Supplementary information

Supplementary Figures

The file contains Supplementary Figures 1-4 with Legends. In Supplementary Figure 1 it is shown that GFP-positive CBC cells in the small intestine of LGR5-Ires-CreERT2 knock-in mice are frequently Ki67 positive, confirming that they are typically cycling cells. The general strategy used to generate the LGR5-Ires-CreERT2 knock-in mice is outlined in Supplementary Figure 2. In Supplementary Figure 3 it is demonstrated that CBC cells and +4 cells differ in their relative sensitivity to radiation-induced apoptosis, confirming that they are distinct cell types. Lgr5-positive CBC cells permanantly marked by the genetic activation of a lacZ reporter gene generate a stream of blue progeny migrating from the crypts onto the villi. This phenomenon is readily visible as blue ribbons on the whole mount pictures in Supplementary Figure 4. (PDF 2162 kb)

Supplementary Video

The file contains Supplementary Video 1. This movie shows a confocal 3D reconstruction of an Lgr5 GFP-positive crypt (inverted). Approximately six GFP-positive CBC cells are visible as wedge-shaped cells located at the base of the crypt. Nuclei are counterstained in red. (MOV 1419 kb)

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

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