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Intestinal crypt homeostasis revealed at single stem cell level by
in vivo live-imaging
Laila Ritsma#1,2, Saskia I.J. Ellenbroek#1,2, Anoek Zomer1,2, Hugo J. Snippert2,3, Frederic J.
de Sauvage4, Benjamin D. Simons5,6,7, Hans Clevers1,2, and Jacco van Rheenen1,2
1Hubrecht Institute-KNAW & University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT, Utrecht,
the Netherlands 2Cancer Genomics Netherlands 3University Medical Centre Utrecht,
Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands 4Department of Molecular Biology,
Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA 5Cavendish Laboratory,
Department of Physics, J.J. Thomson Avenue, University of Cambridge, Cambridge CB3 0HE,
UK. 6The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis
Court Road, Cambridge CB2 1QN, UK. 7Wellcome Trust-Medical Research Council Stem Cell
Institute, University of Cambridge, UK.
# These authors contributed equally to this work.
Summary
The rapid turnover of the mammalian intestinal epithelium is supported by stem cells located
around the base of the crypt1. Alongside Lgr5, intestinal stem cells have been associated with
various markers, which are expressed heterogeneously within the crypt base region1-6. Previous
quantitative clonal fate analyses have proposed that homeostasis occurs as the consequence of
neutral competition between dividing stem cells7-9. However, the short-term behaviour of
individual Lgr5+ cells positioned at different locations within the crypt base compartment has not
been resolved. Here, we established the short-term dynamics of intestinal stem cells using a novel
approach of continuous intravital imaging of Lgr5-Confetti mice. We find that Lgr5+ cells in the
upper part of the niche (termed ‘border cells’) can be passively displaced into the transit-
amplifying (TA) domain, following division of proximate cells, implying that determination of
stem cell fate can be uncoupled from division. Through the quantitative analysis of individual
clonal lineages, we show that stem cells at the crypt base, termed ‘central cells’, experience a
survival advantage over border stem cells. However, through the transfer of stem cells between the
border and central regions, all Lgr5+ cells are endowed with long-term self-renewal potential.
These findings establish a novel paradigm for stem cell maintenance in which a dynamically
heterogeneous cell population is able to function long-term as a single stem cell pool.
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Correspondence and requests for materials should be addressed to J.v.R. (j.vanrheenen@hubrecht.eu) or H.C.
(h.clevers@hubrecht.eu).
Author contributions J.v.R. and L.R. conceived the study. L.R. optimized the surgical and imaging procedure. L.R., S.I.J.E, A.Z, and
H.J.S. performed imaging experiments. L.R., H.J.S., B.D.S., S.I.J.E. performed analyses. F.R.S. provided the Lgr5DTR:EGFP mice
and B.D.S. did all biophysical modelling. L.R. and S.I.J.E. made the figures. J.v.R. and H.C. have supervised the study. All authors
discussed results and participated in preparation of the manuscript.
Full Methods and any associated references are available in the online version of the paper.
Reprints and permissions information is available at ww.nature.com/reprints.
The authors declare no competing financial interests Readers are welcome to comment on the online version of the paper.
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Author Manuscript
Nature. Author manuscript; available in PMC 2014 September 20.
Published in final edited form as:
Nature. 2014 March 20; 507(7492): 362–365. doi:10.1038/nature12972.
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In the small intestine, stem cells are associated with Lgr5 expression, which marks around
14-16 proliferative ‘Crypt Base Columnar (CBC)’ cells distributed throughout the crypt
base. The stem cell niche is constituted by Paneth cells10,11 and surrounding mesenchyme12.
Cells that become displaced from this region enter the TA compartment and lose stemness13.
Quiescent or slow-cycling cells, positioned at or near the ‘+4 position’ may constitute a
second stem cell type3,5,6,14, although a recent study indicated that some, if not all, of these
cells represent secretory precursors that, in common with Dll1+ cells higher in the crypt15,
can be recruited back into the stem cell compartment upon damage16. Hierarchy,
heterogeneity, and spatial organization of intestinal stem cells remain a subject of
debate17-21. Are stem and progenitors organized in an engrained proliferative hierarchy,
defined by a signature of molecular markers, or do stem cells transit reversibly between
states of variable competence in which they become biased towards renewal or
differentiation? If the latter is true, is bias controlled by intrinsic heterogeneity in the
expression of fate determinants, or the consequence of spatio-temporal cues associated with
niche-derived signals? Although inducible genetic lineage tracing allows to dissect short-
term heterogeneity in self-renewal potential, its reliability may be undermined by transient
effects due to drug-inducing agents, Cre activity, or non-representativeness of labelling22.
Therefore we applied an in vivo live-imaging strategy, allowing measurements to begin
several days after drug administration. In common with previous live-imaging approaches
used to study stem cells in hair follicle and testis 23,24,25, our approach enables tracing of the
fate of individual marked stem cells and their progeny over time in vivo.
Multiphoton intravital microscopy and surgical implantation of an abdominal imaging
window (AIW)26,27 into living Lgr5EGFP-Ires-CreERT2/R26R-Confetti mice were used to
obtain visual access to the intestinal stem cell niche (Fig. 1a). Lgr5+ CBC cells and their
progeny were lineage traced over time (Extended Data Fig. 1) by activating the expression
of one of the Confetti colours (membranous CFP, cytoplasmic YFP and RFP) in individual
Lgr5+ cells using Tamoxifen-mediated recombination of the Confetti-construct (Fig. 1a). To
characterize fate behaviour of CBC cells we followed lineages of 80 marked cells (n = 4
mice) up to 5 days from the start of time-lapse imaging (Extended Data Fig. 2, for controls
see 27 and Extended Data Fig. 3).
Following induction, clonal progeny were observed throughout the stem cell niche. To
quantify fate behaviour of Lgr5+ CBC cells, we acquired Z-stacks (Fig. 1b; see Video 1 for
the 3D reconstruction) and classified cells based upon their relative position, using the most
basal cells (termed ‘row 0’) as a reference (Fig. 1b). Confetti-labelled clones were scored
according to cell number, disaggregated by position (Extended Data Fig. 4). In line with
predictions of neutral competition7, numbers of marked cells in the stem cell niche varied
widely between clones (some expanded in size, others lost attachment to this compartment
altogether; Extended Data Figs. 2 and 4). As just 1 of the 28 clones containing a single
marked CBC cell at the start of filming remained single after two days of tracing, we chose
to neglect the potential impact of lineage committed quiescent Lgr5+ cells, identified
previously16.
To investigate spatial heterogeneity in self-renewal potential of CBC cells, we defined two
regions within the Lgr5+ stem cell niche: a central (rows 0 to +2) and border (+3 and +4)
region (Fig. 1b). A ‘mother’ cell in either central or border region could expand and give
rise to progeny that extended into both regions (Fig. 1c-f and Extended Data Fig. 5). Further
quantitative analysis was necessary to address the potency of CBC cells in these two
domains. While the average number of central cells per clone derived from a single central
‘mother’ cell remained approximately constant, consistent with their maintenance over time,
the average number of border cells derived from these cells increased to approximately 2 by
day 3 (Fig. 2a). Furthermore, maintenance of the average central cell number was achieved
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through the steady decline in the number of clones retaining at least one central cell (Fig.
2b), compensated by a steady increase in size of those that remain (Fig. 2c). Although clones
derived from single border ‘mother’ cells also appeared to approximately maintain their
number, they gave rise to a comparatively smaller number of central cells (Fig. 2a). The
sustained increase in the number of border cells from a central ‘mother’ cell (Fig. 2a)
indicates that these cells typically outcompete cells at the niche border (Fig. 2d).
To investigate the potential basis of this positional advantage, we studied the development
of clones with finer time resolution. Every two hours, we acquired multiphoton images of
crypts, followed the location of all GFP-labelled cells over time (Extended Data Fig. 6;
Video 2-4) and found that division of single Lgr5+ cells coincides with displacement of
proximate CBC cells. This suggests that cell proliferation creates competition for space
leading to an adjustment of cell positions. Through this rearrangement, and independent of
their division history, CBC cells located at the border can become passively displaced from
the niche following division of a neighbour (Fig. 2e and Extended Data Fig. 4).
To challenge this conclusion and address the potency of the Lgr5+ CBC stem cell
population, we aimed to quantitatively capture the variability seen in the lineage potential of
individual cells by a biophysical model, involving a revision of the neutral drift dynamics
model introduced in [7,8] in which all stem cells were considered functionally equivalent. In
this new model, a periodic quasi-one-dimensional arrangement of stem cells mimicked the
‘collar-like’ geometry of the central and border niche regions of the crypt (Fig. 3a). To
account for the mixed GFP expression profile seen at rows +3 and +4 (Fig. 1b), the border
region was further subdivided into Lgr5+ CBC cells and Lgr5− TA cells. To accommodate
the range of observed dynamical behaviours in the stem cell niche, we allowed for five
possible ‘channels’ of stem cell loss and replacement (Fig. 3a): Following division of a
border stem cell, one daughter cell remains at its position while the other either (1),
displaces a border TA cell out of the niche; (2), displaces a border stem cell which in turn
displaces a border TA cell out of the niche; or (3), displaces a central stem cell which in turn
displaces a border stem cell into the border TA cell domain. Similarly, after division of a
central stem cell, one daughter remains at its position while the other either (4), displaces a
border stem cell into the border TA cell region; or (5), displaces a central cell which in turn
displaces a border stem cell into the TA cell region. If we define as λ the rate of transfer of
border TA cells out of the niche, each of these 5 processes occur at rates Pb
λ
, Pbb
λ
, Pbc
λ
,
Pcb
λ
, and Pcc
λ
, respectively, with Pb+Pbb+Pbc+Pcb+Pcc=1 (Supplementary Notes).
By fixing the relative rates of stem cell division and displacement by the observed average
clone size dependences and independent estimates of the average cell division rate, we
found that the biophysical model can accurately predict clone size distribution and spatial
dependencies observed in live-imaging (Fig. 2a-c and Fig. 3b, and Extended Data Fig. 7).
More significantly, with the same parameters, the model describes quantitatively
convergence onto the hallmark scaling behaviour reported using static lineage tracing assays
at intermediate times7 (7 and 14 days post-induction), as well as the predicted progression
towards crypt monoclonality at long-times8 (Extended Data Fig. 8 and 9; Supplementary
Notes).
To further challenge the model, we traced the recovery of stem cells following targeted
ablation of Lgr5+ cells using diphtheria toxin (DT) injection in mice where the human DT
receptor (DTR) fused to EGFP was knocked in the Lgr5 locus (Lgr5DTR:EGFP)28 (Fig. 4a).
In these mice, recovered Lgr5+ cells are derived from a TA-lineage28. Following complete
depletion (Fig. 4a), we observed a low frequency of initiation and a heterogeneous pattern of
recovery (Fig. 4b and Supplementary Video 5), suggesting sporadic transfer of cells from
the TA zone into the stem cell niche border. The cohesion of these recovered cell clusters
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(Supplementary Video 6) suggests clonal expansion of individual TA cells. Intriguingly, by
allowing individual border stem cells to recolonize a depleted stem cell niche through cell
division uncompensated by loss, our biophysical model provided a quantitative prediction of
cluster composition (border versus central) by size, with the same relative rates of stem cell
division as those found in steady-state (Fig. 4c and Supplementary Notes).
Our data shows that intestinal stem cell maintenance follows from competition between
proximate CBC stem cells for limited niche access and stem cells positioned near the niche
boundary experience a bias towards loss and replacement, while stem cells remote from the
boundary are biased towards survival. Intriguingly, a similar dependence of self-renewal
potential on proximity to the niche border was reported in a recent in vivo live-imaging
study of mouse hair follicle29, suggesting that such heterogeneity may be a ubiquitous
feature of adult stem cell populations. A recent lineage tracing study based on the
continuous and sporadic acquisition of mutations during DNA replication, concluded that
only a subfraction of putative intestinal stem cells are ‘functional’30. Our quantitative
analysis of live-imaging data shows that central stem cells are about 3 times more likely than
border cells to fully colonize a crypt in steady-state, explaining why only a fraction of Lgr5+
cells appears to retain long-term self-renewal potential (Supplementary Notes). Through the
transfer of cells between the central and border regions of the niche, the dynamic and
heterogeneous population of intestinal stem cells is able to function long-term as a single
equipotent pool.
Online-only Methods
Mice
All experiments were carried out in accordance with the guidelines of the Animal Welfare
Committee of the Royal Netherlands Academy of Arts and Sciences, the Netherlands. To
obtain R26R-Confetti; Lgr5-EGFP-Ires-CreERT2 mice, R26R-Confetti7 mice were crossed
with Lgr5-EGFP-Ires-CreERT21. Random double heterozygous male mice between 10-22
weeks old were used for experiments. Three days before imaging, mice were injected with
2.5-5 mg Tamoxifen (single injection; Sigma Aldrich) to induce activation of Cre
recombinase to induce expression of one of the Confetti colours (membranous CFP,
cytoplasmic YFP and RFP). Nuclear GFP was also activated, but that subset of confetti-
labelled cells was not followed. For the targeted ablation studies, 4 male Lgr5DTR:EGFP mice
carrying an AIW received 50 μg kg−1 diphtheria toxin (DT) through intraperitoneal
injections. Depletion of Lgr5+ cells was confirmed by intravital imaging. Mice in which
Lgr5+ cells were not completely depleted after 24 hours received a second DT injection.
Mice were housed under standard laboratory conditions and received food and water ad
libitum.
AIW surgery
The AIW surgery was performed as described in reference26. In short, all surgical
procedures were performed under 2% isoflurane (v/v) inhalation anaesthesia. Before
surgery, buprenorphine (3 μg per mouse; Temgesic©, BD pharmaceutical limited) was
administered intramuscularly. The left lateral flank of the mice was shaved and the skin was
disinfected with 70% (v/v) ethanol. Next, a left lateral flank incision was made through skin
and abdominal wall and a purse string suture was placed along the wound edge. A
disinfected AIW (> 1 hour in 70% (v/v) ethanol) was placed glass side down next to the
mice and the ileum was placed on top. 3M™ Vetbond™ Tissue Adhesive (n-butyl
cyanoacrylate; 3M) was used to fix the ileum to the cover glass of the AIW and CyGel
(BioStatus Limited) was added to diminish peristaltic movement. After 5 min the AIW was
inverted and placed in the mouse, with the skin and abdominal wall placed inside the AIW
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groove. Then sutures were tightened to stably secure the window into the animal. After
surgery the mice were provided food and water ad libitum. Furthermore, mice were closely
monitored once a day before imaging for behaviour, reactivity, appearance and defecation.
Equipment and settings
Intravital imaging was performed on an inverted Leica TCS SP5 AOBS two-photon
microscope with a chameleon Ti:Sapphire pumped optical parametric oscillator (Coherent
Inc.) equipped with a 25x (HCX IRAPO NA0.95 WD 2.5mm) water objective and four non-
descanned detectors (NDDs). The NDDs collect the following wavelengths: NDD1 <455
nm, NDD2 455-490 nm, NDD3 500-550 nm, NDD4 560-650 nm. Sequential scanning was
performed, exiting the tissue with 860 and 960 nm wavelengths. The Confetti colours were
detected as follows: 860 nm: NDD2 (CFP and eGFP), 960 nm: NDD3 (eGFP and YFP),
NDD4 (YFP and RFP). Second harmonic generation (SHG) signal is generated by 960 nm
excitation at collagen I and detected in NDD2. Scanning was performed in a bidirectional
mode at 700 Hz and 12 bit, with a zoom of 1.7, 512×512 pixels. Z-stacks with 2.5 μm z-
steps of typically 70-80 images were acquired. Re-identification of the same crypts over
multiple days was accomplished by storing the xy coordinates of the imaged regions using
the ‘multiple position’ function in the LAS-AF software and using the vasculature and the
typical (Confetti) Lgr5+ crypt pattern as visual landmarks.
Multi-day intestinal stem cell imaging
After placing the AIW the mice were kept under anaesthesia and placed face-down in a
custom-designed imaging box in which isoflurane (1% (v/v) was administered through a
facemask as described before26. For the multi-day imaging sessions (all imaging figures
except Extended Data Figure 6), mice were imaged once a day for a maximum of 3 hours
during which the climate chamber surrounding the microscope was kept at 32°C. After the
imaging session the mice were allowed to wake up to maintain their body temperature. After
imaging, acquired z-stacks were corrected for z and xy shifts using a custom-designed Visual
Basic software program and further processed and analysed using basic functions in ImageJ
software (linear contrasting, blurring, median filtering).
Short-term intestinal stem cell imaging
Mice were anesthetized using isoflurane (2% v/v). The left lateral flank was shaved and the
skin was disinfected using 70% (v/v) ethanol. Next, a left lateral flank incision was made
through skin and abdominal wall and the ileum was extracorporated using in PBS-drowned
cotton swabs. The ileum was placed on a custom-designed inset containing a coverslip
fitting the custom-designed imaging box. The ileum was secured to the cover slip using
Vetbond and CyGel. The mouse was placed on top of the intestine and in PBS-drowned
sterile cotton gauzes were placed next to the animal to prevent dehydration. Parafilm®M
(Sigma-Aldrich) was used to cover the mouse and a subcutaneous infusion system was used
to provide 100 μl of sterile PBS per hour. The inset was placed within the custom-designed
imaging box in which isoflurane (1%) v/v) was administered through a facemask as
described above. The temperature of the mouse was monitored during imaging using a rectal
probe and was kept between 36 and 37°C by adjusting the temperature of the surrounding
climate chamber. Imaging was performed every 2 hours for 14 hours. Z-stacks with a z-step
of 2.5 μm of 12 regions with on average 6 crypts were made. Acquired z-stacks were
analysed using ImageJ plugins (TurboReg, 3D visualization, 3D viewer).
Intravital imaging of Lgr5+ depleted mice
Mice carrying an AIW received 50 μg kg−1 diphtheria toxin (DT) through intraperitoneal
injections. Depletion of Lgr5+ cells was confirmed by intravital imaging. Mice in which
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Lgr5+ cells were not completely depleted after 24 hours received a second DT injection.
Only mice in which full depletion was confirmed by intravital imaging 24 hours after the
last DT injection were analyzed. The number of Lgr5+-GFP cells within the stem cell niche
border and centre was determined as described in Fig. 1b.
Real-time lineage tracing – clonal competition strength and positional effect on clone size
The data from the lineage tracing was collected at random, and all clones that were imaged
with a 3-day interval were included. The strength of a Confetti-labelled Lgr5+ CBC cell to
produce offspring was expressed as the fold increase in Confetti-labelled Lgr5+ CBC cell
number three days after the first imaging session. A Mann Whitney U test was performed
because the data was not normally distributed.
Quantitative data analysis - Multi-day lineage tracing of Lgr5+ CBC cells
Lineage tracing was performed for 80 clones in 80 crypts from 4 mice. No sample size
estimate was calculated before the study was executed. Only data from mice from which
high enough quality images were acquired were included in the study. The number of
Confetti-labelled cells per crypt position (centre (rows 0 to +2), border (rows +3 to +4), TA
(rows >4)) was scored. From the 80 lineages, we obtained 33 sublineages originating from
the central region (Fig. 4A), and 47 sublineages from the border (Fig 4.B).
Immune cell analysis on intestinal tissue to test potential side-effects of AIW
Six E-Cadherin-CFP/Lgr5EGFP-Ires-CreERT2 mice, 22 weeks of age, were randomly divided
into two groups: a control and a window group. AIWs were implanted on top of the small
intestines of mice from the window group whereas mice from the control group did not
undergo surgery. After 24 hours all mice were sacrificed and the small intestines were
harvested. Note that in the window group the part of the small intestine that was located
directly behind the window was harvested. The small intestines were fixed for 1 day in
fixation mix (1% paraformaldehyde, 0.2% NaIO4, 61mM Na2HPO4, 75mM L-Lysine and
14 mM NaH2PO4 in H2O). After fixation, the tissues were placed for 6 hours into 30%
sucrose after which the tissues were snap-frozen using Tissue Freezing Medium (Leice
Microsystems Nussloch GmbH). 16 μm sections were cut using a Leica CM3050 cryotome.
A standard immunohistochemistry protocol was used to stain the sections with CD45
antibodies (BD Pharmingen™, 553078, Clone 30-F11) and random areas were imaged. For
analysis, 10 areas within the imaged regions were selected and analysed in a blinded
manner. The number of CD45 positive cells within a region was counted manually and an
averaged number for each mouse was calculated. Next, the average of the 3 mice per group
was calculated. A Mann-whitney U test was performed because the sample was not
distributed normally, and no significant differences were found. The variance between the
groups was tested with an F-test, and was not different.
Clone frequency window versus control mice to test potential side-effects of AIW
Eight Lgr5-EGFP-Ires-CreERT2 mice, 22 weeks of age, were divided into two groups: a
control and a window group. All mice received 5 mg Tamoxifen by intraperitoneal injection.
Three days later, AIWs were implanted on top of the small intestines of mice from the
window group whereas mice from the control group did not undergo surgery at this point.
Two days after the surgery (five days after Tamoxifen injection) all mice were imaged. In
the control group the intestine was exteriorized prior to imaging (as described in short-term
intestinal imaging). In the window group the mice were imaged through the AIW. Several
random areas were imaged. All recorded clones were used for analysis. For a single clone
the number of cells within the stem cell compartment was determined and a frequency
distribution was made for the two groups.
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Supplementary Material
Refer to Web version on PubMed Central for supplementary material.
Acknowledgments
The authors would like to thank Anko de Graaff from the Hubrecht Imaging Center for imaging support, all
members of the van Rheenen group for useful discussions and the Hubrecht Institute animal caretakers for animal
support. This work was supported by a Vidi fellowship (91710330; J.v.R.) and equipment grants (175.010.2007.00
and 834.11.002; J.v.R.) from the Dutch organization of scientific research (NWO), a grant from the Dutch cancer
society (KWF; HUBR 2009-4621; J.v.R.), a grant from the Association for International Cancer Research (AICR;
13-0297; J.v.R.), and the Wellcome Trust (grant number 098357/Z/12/Z; B.D.S.).
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Intestinal Crypts and Adenomas. Cell Stem Cell. 2013
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Figure 1. Intravital lineage tracing of Lgr5+ cells
a, Cartoon showing a mouse carrying an abdominal imaging window (AIW) to visualize
intestinal Lgr5+ CBC cells and their Confetti progeny over multiple imaging sessions. b,
Lateral projection of a Z-stack and representative XY-images of a crypt at indicated Z-stack
positions. The stem cell niche (Z0-13) is defined by Lgr5-GFP fluorescence. The relative
position of CBC cells to the most basal cell (row 0) determines location in the central (row 0
to +2, which translates to Z0-6) or border region (row +3 to +4, which translates to Z7-13)
of the stem cell niche. Scale bar, 20 μm. c-f, Intravital lineage tracing of RFP-expressing
Lgr5+ CBC cells located at the centre (c,d) and border (e,f) region. Grey lines indicate
crypts, white lines indicate Confetti clones. (d,f) Graphs show time evolution of spatial
organization of Confetti clones starting 3 days post-induction. Clone size is divided in
central (light green) and border (dark green) CBC cells. Asterisk indicates clones in which
all progeny were lost. Scale bar, 20 μm.
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Figure 2. Central CBC cells experience a short-term positional advantage in self-renewal
potential
a-c, Clonal evolution of a Confetti cell located at the central or border region starting 3 days
post-induction. Graphs show: a, average clone size; b, fraction “surviving” clones that
contain at least one marked central (top) or border (lower) cell; and c, average size of
surviving clones (clones with at least one marked cell). Different colours indicate different
regions in the niche. Points show data and lines show fit to the biophysical model (see Fig
3). Error bars represent s.d. d, Fold increase in clone size over three days from a border or
central Confetti+ CBC cell. Note that central stem cells have a positional advantage over
border stem cells. Error bars represent s.e.m., P <0.001 obtained using a Mann Whitney U
test. e, Intravital images of the same crypt at indicated times. Note that the yellow cell is
truly expelled from the stem cell niche, since GFP-expression was absent in the TA cell
region (see charts at indicated time points). Scale bars, 20 μm.
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Figure 3. Biophysical model of intestinal stem cell dynamics
a, From the unfolded crypt caricature (left), we synthesize a quasi-one-dimensional
biophysical model of the niche region (right) consisting of two domains: border and centre.
To conserve cell number, cell rearrangements following stem cell division displace precisely
one cell from the border. To capture the range of lineage data, we include 5 channels of stem
cell loss/replacement (1-5) defined in the main text. b, Cumulative size distributions of
clones derived from a single cell in the centre (left) or border (right). Clone size is defined in
both cases by total number of constituent cells in centre and border. Error bars represent
s.e.m. Points represent predictions of the model using the same parameters as that inferred
from the average dependences (Supplementary Notes).
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Figure 4. Recovery of stem cell compartment following ablation of Lgr5+ cells challenges model
a, Targeted ablation of Lgr5+ cells in Lgr5DTR:EGFP mice was induced by injection of
diphtheria toxin. Shown are representative images pre- and post-ablation. Scale bars, 20 μm.
b, Recovery of Lgr5+ CBC cells was monitored only in mice where full depletion was
confirmed 24 hours after diphtheria toxin injection. Images taken at 72 hours after depletion
show representative crypts containing clonal clusters of different sizes (n = 108 crypts in 3
mice). Scale bars, 20 μm c, For all various clone sizes, measured spatial composition (border
versus centre) of Lgr5+ CBC cells in clusters (grey) were accurately predicted by the
biophysical model (black). Error bars represent s.d.
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