Retrograde movements determine effective stem cell numbers in intestinal crypts
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE194250 | GEO | 2022/04/20
REPOSITORIES: GEO
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Project description:Retrograde movements determine effective stem cell numbers in intestinal crypts
| PRJNA799997 | ENA
Project description:The effort to better understand intestinal stem cell (ISC) identity and regulation remains a challenge. We have been studying the RNA-binding protein MEX3A as a putative ISC marker. In that context, we have generated the first Mex3a knockout (KO) mouse model and show MEX3A is crucial for maintenance of the Lgr5+ ISC pool. As part of a phenotypic characterization pipeline, we have performed transcriptomic profiling (RNA-sequencing) of isolated Mex3a KO small intestinal crypts and compared it against small intestinal crypts isolated from age-matched wild-type controls.
2020-02-13 | GSE141191 | GEO
Project description:Homeostasis of self-renewing small intestinal crypts results from neutral competition between Lgr5 stem cells, small cycling cells located at crypt bottoms1, 2. Lgr5 stem cells are interspersed between terminally differentiated Paneth cells, that are known to produce bactericidal products such as lysozyme and cryptdins/defensins3. Single Lgr5-expressing stem cells can be cultured to form long-lived, self-organizing crypt-villus organoids in the absence of non-epithelial niche cells4. Here, we note a close physical association of Lgr5 stem cells with Paneth cells in vivo and in vitro. CD24+ Paneth cells express EGF, TGF?, Wnt3 and the Notch-ligand Dll4, all essential signals for stem cell maintenance in culture. Co-culturing of sorted stem cells with Paneth cells dramatically improves organoid formation. This Paneth cell requirement can be substituted by a pulse of exogenous Wnt. Genetic removal of Paneth cells in vivo results in the concomitant loss of Lgr5 stem cells. In colon crypts, CD24+ cells residing between Lgr5 stem cells may represent the Paneth cell equivalents. We conclude that Lgr5 stem cells compete for essential niche signals provided by a specialized daughter cell, the Paneth cell. We used intestinal cell fractions from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations: stem cells were sorted based on high level of GFP expression (GFPhi) and Paneth cells were sorted based on high level of CD24 expression (CD24hi) and high side-scatter (SSChi). Differentially labelled cRNA from GFPhi and CD24hi/SSChi cells from two different sorts (each combining ten individual mice) were hybridized on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments, resulting in four individual arrays.
2010-11-29 | E-GEOD-25109 | biostudies-arrayexpress
Project description:Homeostasis of self-renewing small intestinal crypts results from neutral competition between Lgr5 stem cells, small cycling cells located at crypt bottoms1, 2. Lgr5 stem cells are interspersed between terminally differentiated Paneth cells, that are known to produce bactericidal products such as lysozyme and cryptdins/defensins3. Single Lgr5-expressing stem cells can be cultured to form long-lived, self-organizing crypt-villus organoids in the absence of non-epithelial niche cells4. Here, we note a close physical association of Lgr5 stem cells with Paneth cells in vivo and in vitro. CD24+ Paneth cells express EGF, TGFα, Wnt3 and the Notch-ligand Dll4, all essential signals for stem cell maintenance in culture. Co-culturing of sorted stem cells with Paneth cells dramatically improves organoid formation. This Paneth cell requirement can be substituted by a pulse of exogenous Wnt. Genetic removal of Paneth cells in vivo results in the concomitant loss of Lgr5 stem cells. In colon crypts, CD24+ cells residing between Lgr5 stem cells may represent the Paneth cell equivalents. We conclude that Lgr5 stem cells compete for essential niche signals provided by a specialized daughter cell, the Paneth cell.
2010-11-29 | GSE25109 | GEO
Project description:Gene inactivation of the orphan G protein-coupled receptor Lgr4, a paralog of the epithelial stem cell marker Lgr5, results in 50% decrease of epithelial cell proliferation and 80% reduction in terminal differentiation of Paneth cells in postnatal mouse intestinal crypts. When cultured ex vivo, Lgr4-deficient crypts or progenitors, but not Lgr5-deficient progenitors, die rapidly with dramatic downregulation of stem cell markers and Wnt target genes, including Lgr5. Partial rescue of this phenotype is achieved by LiCl addition to the culture medium, but not by Wnt agonists. Our results identify Lgr4 as a permissive factor of the Wnt pathway in the intestine and, as such, as a potential target for intestinal cancer therapy. Microarray hybridization was performed on LGR4 KO intestinal crypts at day 0, day 0.5 and day 1 versus wild-type crypts. The effects of LiCl treatment on LGR4 KO crypts at day1 versus control cells were investigated. After amplification and labelling, sample pairs were hybridized onto Mouse Exonic Evidence Based Oligonucleotide (MEEBO) arrays containing on average 38784 mouse 70mer oligonucleotide probes (Stanford University, US). Hybridizations were replicated with dye swap.
2012-03-10 | E-GEOD-27904 | biostudies-arrayexpress
Project description:Intestinal stem cells (ISCs) residing in the crypts are critical for the continual self-renewal and rapid recovery of intestinal epithelium. The regulatory mechanism of ISCs is not fully understood. Here we report that CREPT, a recently identified tumor-promoting gene, is preferably expressed in the crypts, where the ISCs reside, but not in the villi. The Lgr5+ ISCs have much higher CREPT protein level than Lgr5- cells. To explore the function of CREPT in ISCs, we isolated WT and CREPT deleted Lgr5+ ISCs (Lgr5-CREPTKO) to perform Next generation sequencing.
2020-11-08 | GSE143604 | GEO
Project description:Wnt signals control three functions of intestinal crypts: maintenance of Lgr5 stem cells, proliferation of transit-amplifying daughters and formation of Paneth cells. Here, we study how the Wnt effector β-catenin/Tcf4 cooperates with the Wnt-activated transcription factor Ascl2 to control a stem cell transcription program. DNA elements that are co-occupied and synergistically regulated by Ascl2 and Tcf4 specifically map to stem cell genes. In vitro, Tcf4-/- mini-guts are rescued by Ascl2 expression, while Ascl2-/- organoids are rescued by Wnt signaling. A direct auto-activatory loop leads to an on/off expression pattern of Ascl2 with a threshold that depends on the previous state. Wnt/R-spondin1 activates this loop. This mechanism interprets Wnt levels in crypts and translates this continuous signal into a discrete Ascl2 âonâ or âoffâ decision. In turn Ascl2, together with β-catenin/Tcf, activates stem cell genes. Thus, Ascl2 forms a transcriptional 'stemness switch' that is both Wnt-responsive and Wnt-dependent Examination of Tcf4, B-catenin and Ascl2 DNA occupancy in murine intestinal organoids and human colorectal cancer cell lines *** Original raw files unavailable due to loss during backup ***
2016-07-15 | E-GEOD-84456 | biostudies-arrayexpress
Project description:The intestinal epithelium is the most rapidly self-renewing tissue in adult mammals. We have recently demonstrated the presence of approximately six cycling Lgr5+ stem cells at the bottoms of small intestinal crypts1. We have now established long-term culture conditions under which single crypts undergo multiple crypt fission events, whilst simultanously generating villus-like epithelial domains in which all differentiated cell types are present. Single sorted Lgr5+ stem cells can also initiate these crypt-villus organoids. Tracing experiments indicate that the Lgr5+ stem cell hierarchy is maintained in organoids. We conclude that intestinal crypt-villus units are self-organizing structures, which can be built from a single stem cell in the absence of a non-epithelial cellular niche. Keywords: expression profiling Freshly isolated small intestinal crypts from two mice were divided into two parts. RNA was directly isolated from one part (RNeasy Mini Kit, Qiagen), the other part was cultured for one week according to the conditions described in the associated paper, followed by RNA isolation. We prepared labeled cRNA following the manufacturer’s instruction (Agilent Technologies). Differentially labelled cRNA from small intestinal crypts and organoids were hybridised separately for the two mice on a 4X44k Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments, resulting in four individual arrays.
2009-04-03 | E-GEOD-14594 | biostudies-arrayexpress
Project description:Comparative gene expression profiling between DSS-treated crypts and normal colon crypts Comparative gene expression profiling between normal colon crypts and tumor crypts
2017-01-01 | GSE56050 | GEO
Project description:Regenerative cell state dynamics are under-characterized. Intestinal damage prompts reprogramming into revival stem cells (revSCs) that reconstitute Lgr5+ intestinal stem cells (ISCs). Here, single nuclear multiomics of crypts regenerating from irradiation shows revSC epigenetic profiles overlap with ISCs and differentiated lineages. RevSC genes themselves are accessible throughout homeostatic epithelia, while damage-induced crypt remodelling converges on the Hippo and TGFβ pathway that is transiently activated in the crypt and directly induces functional revSCs. Combinatorial analysis of gene expression suggests multiple sources of revSCs, and we show TGFb can reprogram Enterocytes, Goblet, and Paneth cells into revSCs, further demonstrating individual revSCs form organoids. Despite this, loss of TGFβ signalling yielded mild regenerative defects, whereas interference in both Hippo and TGFβ led to rapid intestinal collapse with no detectable revSCs or ISCs. Regenerative signalling is thus poised for activation by a compensatory system of crypt-localized, transient morphogen cues that support robust intestinal regeneration.
2024-08-19 | GSE230766 | GEO