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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Nat Cell Biol. Author manuscript; available in PMC 2013 October 3.
Published in final edited form as:
PMCID: PMC3789123

Dll1 marks early secretory progenitors in gut crypts that can revert to stem cells upon tissue damage


Lgr5 stem cells reside at small intestinal crypt bottoms, generating both the enterocyte and secretory lineage. Entry into the latter epithelial lineage requires silencing of Notch signaling. The Notch ligand Dll1 is strongly up-regulated in a small subset of immediate stem cell daughters. Lineage tracing utilizing a novel Dll1GFP-ires-CreERT2 knock-in mouse reveals that single Dll1high cells generate small, short-lived clones of all four secretory cell types. In culture, sorted Dll1high cells can form long-lived organoids when briefly exposed to Wnt3A. When Dll1 cells are genetically marked prior to tissue damage, significant numbers of stem cell tracing events occur. Lineage specification therefore occurs already in the earliest stem cell daughters through Notch lateral inhibition. Yet, specified secretory progenitors display plasticity and can regain stemness upon tissue damage.

The intestinal epithelium represents a unique model for the study of adult stem cell biology and lineage specification. Not only is it the fastest self-renewing tissue in mammals with a turn-over time of 5 days, it also has a simple, highly repetitive layout. Lgr5high stem cells are intermingled with Paneth cells at the base of the crypt and feed daughter cells into the Transit Amplifying (TA) compartment that fills the remainder of the crypt (1). TA cells undergo approximately 4–5 rounds of rapid cell division, after which they cross the crypt-villus boundary to terminally differentiate into enterocytes or into one of the secretory cell types, i.e goblet cells, tuft cells and enteroendocrine cells (2-6). The Paneth cells represent a fourth secretory cell type that is unusual in its location at crypt bottoms and its relatively long lifespan of 6-8 weeks (7). Paneth cells serve as niche cells, providing Wnt, Notch and EGF signals to stem cells (8). The first binary fate decision of undifferentiated crypt TA cells involves entry into either the enterocyte or the secretory lineage. A simple molecular circuit downstream of the Notch1/2 receptors controls the absorptive/secretory switch (9). Notch signaling activates Hes1 expression in the receiving cell, typically the crypt stem cell or the undifferentiated TA cells (10-11). HES1 in turn represses expression of the Math1 transcription factor that is crucial for entry into the secretory lineage (12-14). While all TA cells in crypts are capable of converting into secretory cells upon acute blockade of Notch (11,15,16), it is currently not known at what level in the stem cell/TA hierarchy this lineage specification occurs physiologically. Stem cells and the bulk of the TA cells express Notch1 and Notch2 (9), while Delta-like 1 (Dll1) and Delta-like 4 (Dll4) function redundantly as Notch ligands (17).

Dll1 is expressed by rare undifferentiated TA cells that are early descendants of Lgr5 stem cells

While Paneth cells express Dll1 and Dll4, thus activating Notch receptors on adjacent stem cells, it is unclear which cells in the TA compartment express Notch ligands to activate Notch receptors on TA cells. A Dll1 in situ hybridization probe brightly marked rare cells 1-2 cell positions above the stem cell/Paneth cell zone (Fig. 1A). Much weaker signals were obtained in individual cells higher up in the crypt and on the villus. This pattern was reminiscent of zebra fish DeltaD in secretory cells of the intestinal tract (18). The rare scattered Dll1high cells in crypts had the morphology of TA cells.

Fig. 1
Dll1 is expressed by rare undifferentiated TA cells that are early descendants of Lgr5 stem cells

To determine the temporal, hierarchical relationship between the Lgr5 stem cells and these Dll1high cells, we induced lineage tracing in Lgr5GFP-ires-CreERT2 knock-in mice crossed to the Cre reporter R26RLacZ. At various time points post-tamoxifen induction, we analyzed the expression of the stem cell marker gene Lgr5, the Cre reporter LacZ and Dll1 by triple color mRNA in situ hybridization at single cell resolution (19). We thus noted that 1-2 days after the induction of lineage tracing in stem cells, Dll1high cells were first observed within the marked clone (Fig. 1C versus 1B). This indicated that –as expected- Dll1high cells derive from Lgr5+ stem cells. More importantly, the time course revealed that Dll1high cells derive from stem cells within 1-2 cell divisions, given that Lgr5 stem cells divide every 24 hours (20). This was consistent with the physical position of the Dll1high cell, immediately above the stem cell/Paneth cell zone.

To study Dll1+ cells, we integrated a GFP-ires-CreERT2 cassette into the start codon of the Dll1 locus (Suppl. Fig. 1). Heterozygous knock-in mice were healthy and fertile and GFP appeared faithfully expressed as assessed by confocal analysis (Fig. 1D). This analysis showed the presence of rare GFP+ cells 1-2 cell cells above the stem cell/Paneth cell zone as well as higher up the crypts and villi (Fig. 1E).

Dll1+ cells, obtained by Fluorescence-Activated Cell Sorting (FACS) for GFP and for levels of CD24 expression, were subjected to microarray analysis. This revealed that Dll1GFP+CD24high, and Dll1GFP+CD24low cells correspond to Paneth cells, and enteroendocrine/goblet cells, respectively (Fig. 1E and Suppl. Fig. 2). The Dll1GFP+CD24mid cells expressed markers of multiple secretory lineages, suggesting that these cells represent secretory progenitors. Importantly, Dll1GFP+CD24mid cells expressed high levels of Math1 and very low levels of Notch1, Notch2 and Hes1, indicative of an inactive Notch signaling pathway (Suppl. Fig. 2). This set them apart from stem cells and the bulk of TA cells that express high levels of Notch1, Notch2 and Hes1 and low levels of Math1 (9,10,14,16).

Dll1high precursor cells generate short-lived clones of mixed secretory cell content

We then performed a lineage tracing study by crossing the Dll1GFP-ires-CreERT2 allele with the Cre reporter allele R26RLacZ. Adult mice were subjected to a single tamoxifen pulse and the proximal small intestine was analyzed histologically 12 hrs and, 2, 4, 10 and 122 days later. After 12 hrs, single LacZ+ cells occurred mainly around the ‘+5’ position, one cell-diameter removed from the uppermost Paneth cell (Fig. 2A and 2B). We concluded that Cre excision was fortuitously restricted to the cells that express highest Dll1 mRNA levels as assessed by in situ hybridization (Fig. 1B) and not by other GFP-expressing cells (Fig. 1D). On day 2, multiple LacZ+ cells occurred at the top of the crypt and the villus base (average 1.4 LacZ+ cells per tracing crypt/villus unit; range 1-3 LacZ+ cells) (Fig. 2C). On day 4, LacZ+ cells mainly occurred on villi (average 3.2 LacZ+ cells per tracing crypt/villus unit; range 1-7 LacZ+ cells), while occasional LacZ+ Paneth cells were first noted (Fig. 2D). On day 10, only LacZ+ Paneth cells remained (Fig. 2E). On day 122 post-induction, we occasionally detected ribbons of LacZ+ cells (average of 9.8 stem cell derived tracings per duodenum), while we never observed tracing in non-induced mice (not shown).

Fig. 2
Lineage tracing of Dll1GFP-ires-CreERT2 × R26RLacZ knock-in intestine

To determine which cell types became LacZ+, Dll1GFP-ires-CreERT2-R26RLacZ mice were induced by tamoxifen injections on 3 sequential days. Marker analysis, performed 4 days later, revealed LacZ+ goblet cells (Fig. 3A), Paneth cells (Fig. 3B), tuft cells (Fig. 3C), and enteroendocrine cells (Fig. 3D). Importantly, we never detected LacZ+ enterocytes. We concluded that the Dll1high cells localized at the ‘+5’ position generate short-lived clones exclusively consisting of secretory lineage cells.

Fig. 3
Intestinal Dll1+ cells are secretory lineage precursors

Using the multi-color Cre reporter R26Rconfetti for tracing (21), we found that a single Dll1+ cell could give rise to mixed secretory clones consisting of 2-6 cells. Examples are given in Fig. 3E and 3F.

Dll1high precursor cells build long-lived organoids when exposed to Wnt

To examine the potential stemness of Dll1+ cells in vitro, we sorted and cultured Dll1GFP+CD24high, Dll1GFP+CD24mid and Dll1GFP+CD24low cells. Under standard crypt culture conditions (EGF, Noggin and R-spondin1 in Matrigel; (22)), none of the Dll1+ FACS-sorted subpopulations generated organoid structures (Fig. 4A), in sharp contrast to sorted Lgr5+ cells (22). However, addition of Wnt-3A enabled Dll1+CD24mid cells, but not Dll1+CD24high or Dll1+CD24low cells, to give rise to organoid structures. Single Dll1GFP+/CD24mid cells derived from Dll1GFP-ires-CreERT2_Lgr5LacZ small intestinal crypts and cultured in the presence of Wnt3A, showed the induction of Lgr5LacZ+ stem cells at the bottom of crypt equivalents (Fig. 4B). Moreover, the presence and location of Dll1GFP+ secretory cells in these organoids mimicked the in vivo situation (Fig. 4C). Taken together, Dll1+CD24mid secretory progenitor cells could regain stemness upon Wnt stimulation in culture.

Fig. 4
Dll1 precursors can convert to intestinal stem cells

Dll1high precursor cells revert to stem cells upon tissue damage

Dll1high precursor cells generate short-lived secretory clones, but rarely generate the “signature” long-lived ribbons that Lgr5high stem cells will (1). The intestine has a unique capacity to regenerate upon extensive damage. We wondered if the Dll1high fated precursor cells would be capable of replacing lost stem cells upon extensive radiation damage. We therefore induced Cre expression with tamoxifen in the Dll1GFP-ires-CreERT2-R26RLacZ mice, one day prior to sublethal irradiation (6.0 Gy gamma at day 0). This dosage of irradiation causes strong reduction of Lgr5+ stem cells and major apoptosis in the intestinal crypt (not shown, and 1). The duodenum was subsequently analyzed by LacZ staining at day 28 post irradiation. At this time point, we normally only observe Dll1+ cell-derived LacZ+ Paneth cells at crypt bottoms. As demonstrated by sectioning (Fig. 4D), stem cell tracing events shown as ribbons of cells emanated from the crypt bottoms which ran up the side of adjacent villi (average of 96.1 stem cell derived tracings per duodenum per mouse)(Fig. 4E). These contiguous ribbons consisted of secretory as well as absorptive cells (i.e. enterocytes). These data unequivocally demonstrated that Dll1high precursor cells can revert to stem cells upon tissue damage. In our control, i.e. tamoxifen induction at day 0 without radiation, we observed occasional complete LacZ+ ribbons which shows that this phenomenon also occasional takes place in a normal intestine (average 9.8 stem cell derived tracings per duodenum per mouse, resp) (Fig. 4E). In our control, i.e. tamoxifen injection at day -14 followed by radiation on day 0, we observed similar number of tracings (average 8.4 stem cell derived tracings per duodenum per mouse) showing that this is a phenomenon which is not caused by Dll1 induction in the intestinal stem cells (Fig. 4E).

In this study, we have investigated Dll1-expressing crypt cells from the perspective of the stem cell hierarchy of the small intestinal epithelium. The cells expressing highest levels of Dll1 typically reside one cell diameter above the top Paneth cell, a position we refer to as “+5”. Lineage tracing using a CreERT2-expressing Lgr5 allele demonstrates that Dll1high cells are immediate descendants of Lgr5+ stem cells. Mice generated to carry a novel allele of Dll1 (by insertion of a cassette containing GFP and CreERT2 into the first coding exon) allowed lineage tracing of Dll1high cells, which were thus shown to generate small, short-lived clones that uniquely consist of cell types of the secretory lineage. Moreover, we found that the Dll1+ cells can revert to stem cells, in vitro when provided with exogenous Wnt signals, and in vivo upon tissue damage.

The following scenario can be scripted. In the stem cell zone, the Dll1+ Dll4+ Paneth cells trigger Notch1 and Notch2 on stem cells, thus keeping the stem cells from terminal differentiation into the secretory lineage (9,17). Each day, each of the 15 stem cells divides and consequently 15 daughter cells exit the Paneth/stem cell zone. These daughters pass through the ‘+5’ position, thereby losing direct access to Delta ligands. Stochastically, some of these cells lose Notch expression, and strongly up regulate Dll1 expression, thereby setting their own secretory fate. Simultaneously, such a cell can present Dll1 to 6-8 neighboring TA cells. These TA cells will thus maintain an active Notch pathway and will stay fated towards the enterocyte lineage. Thus, the enterocyte/secretory switch appears to be controlled through Notch by lateral inhibition. Many examples illustrate this classical mechanism, which typically operates to induce opposite cell fates within fields of initially identical cells (23)

In addition, we identified another characteristic of the Dll1+ cells. In vitro as well as in vivo, these early “fated” progenitors in the intestinal epithelium can revert to stem cells, presumably by regaining proximity to Paneth cells, the source of Wnt, Notch and EGF signals (8). Although not probed here, it appears highly like that the bulk of the TA cells which are underway to become enterocytes rather than secretory cells, can similarly de-differentiate into stem cells. This process of dedifferentiation, or plasticity, is not uncommon. For instance in the Drosophila gonad, both female and male germ cells can regain stem cell identity after initiation of differentiation (24-25). Thus, stemness in the intestine may be regarded as a cellular ‘state’ determined by location, rather than a cellular ‘fate’ determined by history. This plasticity may have implications for views on the occurrence and role of cancer stem cells, as have been described in intestinal cancer (reviewed in 26,27).

Supplementary Material

Supplementary Information


This research was supported by KWF/HUBR2005-3237 (TS), KWF/HUBR2005-3956 (LZ), EU/Health-F4-2007-200720 (MvdW) and EU/232814-StemCellMark (HS).


The authors disclose no conflicts of interest.


[1] Barker N, van Es JH, Kuipers J, Kujala J,P, et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature. 2007;449:1003–1007. [PubMed]
[2] Marshman E, Booth C, Potten CS. The intestinal epithelial stem cell. Bioessays. 2002;24:91–98. [PubMed]
[3] Gerbe F, van Es JH, Makrini L, Brulin B, Mellitzer G, et al. Distinct ATOH1 and Neurog3 requirements define tuft cells as a new secretory cell type in the intestinal epithelium. J Cell Biol. 2011;192:767–780. [PMC free article] [PubMed]
[4] Cheng H, Leblond CP. Origin, differentiation and renewal of the four main epithelial cell types in the mouse small intestine. I. Columnar cell. Am J Anat. 1974;141:461–479. [PubMed]
[5] Bjerknes M, Cheng H. Clonal analysis of mouse intestinal epithelial progenitors. Gastroenterology. 1999;116:7–14. [PubMed]
[6] Cheng H, Leblond CP. 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. 1974;141:537–561. [PubMed]
[7] Ireland H, Houghton C, Howard L, Winton DJ. Cellular inheritance of a Cre- activated reporter gene to determine Paneth cell longevity in the murine small intestine. Dev Dyn. 2005;233:1332–1336. [PubMed]
[8] Sato T, van Es JH, Snippert HJ, Stange DE, Vries RG, et al. Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts. Nature. 2011;469:415–418. [PMC free article] [PubMed]
[9] Riccio O, van Gijn ME, Bezdek AC, Pellegrinet L, van Es JH, et al. Loss of intestinal crypt progenitor cells owing to inactivation of both Notch1 and Notch2 is accompanied by derepression of CDK inhibitors p27Kip1 and p57Kip2. EMBO Rep. 2008;4:377–383. [PubMed]
[10] Jensen J, Pedersen EE, Galante P, Hald J, Heller RS, et al. Control of endodermal endocrine development by Hes-1. Nature genetics. 2000;24:36–44. [PubMed]
[11] van Es JH, van Gijn ME, Riccio O, van den Born M, Vooijs M, et al. Notch/gamma-secretase inhibition turns proliferative cells in intestinal crypts and adenomas into goblet cells. Nature. 2005;435:959–963. [PubMed]
[12] Yang Q, Bermingham NA, Finegold MJ, Zoghbi HY. Requirement of Math1 for secretory cell lineage commitment in the mouse intestine. Science. 2001;294:2155–2158. [PubMed]
[13] Shroyer NF, Helmrath MA, Wang VY, Antalffy B, Henning SJ, et al. Intestine- specific ablation of mouse atonal homolog 1 (Math1) reveals a role in cellular homeostasis. Gastroenterology. 2007;132:2478–2488. [PubMed]
[14] van Es JH, de Geest N,, van de Born M, Clevers H, Hassan BA. Intestinal stem cells lacking the Math1 tumour suppressor are refractory to Notch inhibitors. Nat Commun. 2010;1:8. [PMC free article] [PubMed]
[15] Milano J, McKay J, Dagenais C, Foster-Brown L, Pognan F, et al. Modulation of notch processing by gamma-secretase inhibitors causes intestinal goblet cell metaplasia and induction of genes known to specify gut secretory lineage differentiation. Toxicol Sci. 2004;82:341–358. [PubMed]
[16] Wu Y, Cain-Hom C, Choy L, Hagenbeek TJ, de Leon GP, et al. Therapeutic antibody targeting of individual Notch receptors. Nature. 2010;464:1052–1057. [PubMed]
[17] Pellegrinet L, Rodilla V, Liu Z, Chen S, Koch U, et al. Dll1- and dll4-mediated Notch signaling are required for homeostasis of intestinal stem cells. Gastroenterology. 2011;140:1230–1240. [PMC free article] [PubMed]
[18] Crosnier C, Vargesson N, Gschmeissner S, Ariza-McNaughton L, Morrison A, et al. Delta-Notch signalling controls commitment to a secretory fate in the zebrafish intestine. Development. 2005;132:1093–1104. [PubMed]
[19] Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods. 2008;10:877–879. [PMC free article] [PubMed]
[20] Schepers AG, Vries R, van den Born M,, van de Wetering M, Clevers H. Lgr5 intestinal stem cells have high telomerase activity and randomly segregate their chromosomes. EMBO J. 2011;30:1104–1109. [PubMed]
[21] Snippert HJ, van der Flier LG, Sato T, van Es JH, van den Born M, et al. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell. 2010;143:134–144. [PubMed]
[22] Sato T, Vries RG, Snippert HJ, van de Wetering M, Barker N N, et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature. 2009;459:262–265. [PubMed]
[23] Axelrod JD. Delivering the lateral inhibition punch line: it’s all about the timing. Sci Signal. 2010;3:pe38. [PubMed]
[24] Kai T, Spradling A. Differentiating germ cells can revert into functional stem cells in Drosophila melanogaster ovaries. Nature. 2004;428:564–569. [PubMed]
[25] Brawley C, Matunis E. Regeneration of male germline stem cells by spermatogonial dedifferentiation in vivo. Science. 2004;304:1331–1334. [PubMed]
[26] Davies EJ, Marsh V, Clarke AR. Origin and maintenance of the intestinal cancer stem cell. Mol Carcinog. 2011;50:254–263. [PubMed]
[27] Anderson EC, Hessman C, Levin TG, Monroe MM, Wong MH. The Role of Colorectal Cancer Stem Cells in Metastatic Disease and Therapeutic Response. Cancers. 2011;3:319–339. [PMC free article] [PubMed]