Genome-wide gene-expression profile of mouse intestinal stem cells/progenitors/Paneth cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE122230 | GEO | 2019/07/19
REPOSITORIES: GEO
Similar Datasets
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:The introduction of GFP into the Dll1 locus has made it possible to isolate and study primary intestinal Dll1 positive cells, which constitute the secretory cell precursors of the intestine. Applying DNA array technology, we profiled the RNA changes of FACS-sorted Dll1_high/CD24_low, Dll1_high/CD24_medium and Dll1_high/CD24_high cells . We used cell fractions of intestines from Dll1-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Dll1 promoter. RNA was isolated from three FACS sorted cell populations: all are expressing Dll1-GFP at high levels, but are expressing different levels of Cd24 (low, medium and high). For this set two biological replicates were generated. One additional fraction was isolated from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. This cell fraction contains intestinal stem cells. Differentially labelled cRNA from these cell fractions was hybridized against a reference (RNA isolated from whole intestine) on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F).
2012-09-27 | E-GEOD-39915 | biostudies-arrayexpress
Project description:The impact of removal of Mll1 in intestinal Paneth cells expressing an constitutively active form of beta-catenin (beta-cateninGOF) was analysed in 4 pairs of sorted Paneth cells of Lgr5-CreERT2; beta-cateninGOF;Mll1+/- (control) and Lgr5-CreERT2; beta-cateninGOF;Mll1-/- (knockout) mice at 10 days after tamoxifen-induced mutagenesis. Using 75-base-pair reads, around 30 million reads per sample with comparable unique mapped reads (52-93%) were obtained. To analyze differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. Differentially expressed genes in beta-cateninGOF; Mll1-/- versus beta-cateninGOF; Mll1+/- Paneth cells showed both up- and downregulation of genes at a false discovery rate (FDR) of 10%. This included a global increase in the expression of goblet cell-specific genes. Downregulated genes included specific markers of Paneth cells, indicating that ablation of Mll1 in Paneth cells shifted their identity towards a mixed Paneth-goblet cell fate.
2022-01-08 | GSE177047 | GEO
Project description:The impact of Mll1 removal on the intestinal stem cells and its direct effect on neighbouring Paneth cells was evaluated in sorted intestinal stem and Paneth cells from Mll1FC/+; Lgr5-eGFP-CreERT2/+ (control) and Mll1FC/FC; Lgr5-eGFP-CreERT2/+ (knockout) mice, 4 and 10 days after tamoxifen-induced mutagenesis. Using 75-base-pair reads, 30 million reads per sample with comparable unique mapped reads for stem (70-77%) and Paneth (60-76%) cells were obtained. To analyze differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. Analysis by DAVID and GSEA at a false discovery rate (FDR) of 5% was conducted.The stem cell transcriptome revealed that Mll1 knockout stem cells exhibited a decreased expression of several transcription factors and stem cell genes. Additionally, Mll1 ablation in stem cells had an impact on Paneth cells. Downregulation of Paneth cell specific markers indicated a loss of Paneth cell identity.
2021-11-10 | GSE157285 | GEO
Project description:Paneth cells are a highly specialized population of intestinal epithelial cells located in the crypt adjacent to Lgr5+ stem cells, from which they differentiate through a process that requires downregulation of the Notch pathway. Their ability to store and release antimicrobial peptides protects the host from intestinal pathogens and controls intestinal inflammation. Here we show that PKCλ/ι is required for Paneth cell differentiation at the level of Atoh1 and Gfi1, through the control of EZH2 stability by direct phosphorylation. The selective inactivation of PKCλ/ι in epithelial cells results in the loss of mature Paneth cells, increased apoptosis and inflammation, and enhanced tumorigenesis. Importantly, PKCλ/ι expression in human Paneth cells decreases with progression of Crohn's disease. Kaplan-Meier survival analysis of CRC patients revealed that low PRKCI levels correlated with significantly worse patient survival. Therefore, PKCλ/ι is a negative regulator of intestinal inflammation and cancer through its role in Paneth cell homeostasis.
2017-08-23 | GSE84118 | GEO
Project description:Paneth cells (PCs) are long-lived secretory cells that reside at the bottoms of small intestinal crypts. Besides serving as niche cells for the neighboring Lgr5-positive stem cells, PCs secrete granules containing a broad spectrum of antimicrobial proteins, including lysozymes and defensins1. Here, we have used single-cell RNA sequencing to explore PC differentiation. We found a maturation gradient from early secretory progenitors to mature PCs, capturing the full maturation path of PCs. Moreover, differential expression of a subset of defensin genes in lysozyme-high PCs, e.g. Defa20, reveals at least two distinct stages of maturation. We traced Lgr5+ stem cells from Lgr5-CreERT2 C57Bl6/J mice bred to a Rosa26LSL-YFP reporter mice and sorted YFP+ cells 5 days, 3 weeks and 8 weeks after tamoxifen injection.
2016-06-23 | E-GEOD-76408 | biostudies-arrayexpress
Project description:Gene expression profiles of Lgr5-GFP high and Lgr5-GFP low cells in small intestines of Itgb7+/+ Lgr5-GFP mice and Itgb7-/- Lgr5-GFP mice
| PRJNA552264 | ENA
Project description:Little is known about how pro-obesity diets regulate tissue stem and progenitor cell function. Here we find that high fat diet (HFD)-induced obesity augments the numbers and function of Lgr5+ intestinal stem cells (ISCs) of the mammalian intestine. Like HFD, ex vivo treatment of intestinal organoid cultures with palmitic acid (PA), a constituent of the HFD, enhances the self-renewal potential of these organoid bodies. Mechanistically, HFD induces a robust peroxisome proliferator-activated receptor delta (PPAR-delta signature in intestinal stem and progenitor cells and pharmacologic activation of PPAR-delta recapitulates the effects that HFD has on these cells. Interestingly, HFD- and agonist-activated PPAR-delta signaling endows organoid-initiating capacity to non-stem cells and enforced PPAR-delta signaling permits these non-stem cells to form in vivo tumors upon loss of the tumor suppressor Apc. These findings highlight how diet-modulated PPAR-delta activation alters not only the function of intestinal stem and progenitor cells but also their capacity to initiate tumors. mRNA profiles of intestinal stem cells (GFP-Hi) and progenitors (GFP-Low) from WT or HFD fed mice were generated by deep sequencing using HiSeq 2000.
2016-02-16 | E-GEOD-67324 | biostudies-arrayexpress
Project description:The generation of the Lgr5_EGFP_ires_CreERT2 knock-in mouse allows marking of Lgr5 positive cells of different tissues. Here we use these mice to sort Lgr5 positive cells and their daughter cells form intestinal adenomas and describe the expression profile of these two cell populations. Intestinal adenomas were generated by inducing Apc deletion through tamoxifen injection in Apc_fl/fl-Lgr5_EGFP_ires_CreERT2 mice. In these mice, GFP is expressed under the control of the Lgr5 promoter, leading to highest GFP levels in Lgr5 positive cells (GFP-high). Dividing GFP-high cells pass on Gfp two their daughter cells, thereby diluting the GFP. Daughter cells can therefore be isolated based on their lower GFP positivity (GFP-low). We sorted these two cell fractions (GFP-high and GFP-low) and compared them to each other on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F). Three independent sorts were performed and RNA of GFP-high cells hybridized directly against RNA of GFP-low cells in three dye swap experiments, resulting in six individual arrays.
2012-08-12 | E-GEOD-37926 | biostudies-arrayexpress