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HNF4a acts as upstream functional regulator of intestinal Wnt3 and Paneth cell fate [RNA-seq]

ABSTRACT: Maturation of Paneth cells depends on canonical Wnt signaling, but few transcriptional regulators have been identified to this end. We showed that HNF4a plays a non-redundant and crucial role in supporting the growth and survival of small intestinal epithelial cultures when cultured ex vivo as organoids. Transcriptomic analyses revealed an autosomal function of HNF4a in Wnt3 transcriptional regulation and Paneth cell differentiation. We showed that Wnt3a supplementation reversed cell death and transcriptional changes caused by the deletion of Hnf4a in jejunal organoids.

ORGANISM(S): Mus musculus

PROVIDER: GSE171657 | GEO | 2022/12/01

REPOSITORIES: GEO

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HNF4a acts as upstream functional regulator of intestinal Wnt3 and Paneth cell fate

Project description:Maturation of Paneth cells depends on canonical Wnt signaling, but few transcriptional regulators have been identified to this end. We showed that HNF4a plays a non-redundant and crucial role in supporting the growth and survival of small intestinal epithelial cultures when cultured ex vivo as organoids. Transcriptomic analyses revealed an autosomal function of HNF4a in Wnt3 transcriptional regulation and Paneth cell differentiation. We showed that Wnt3a supplementation reversed cell death and transcriptional changes caused by the deletion of Hnf4a in jejunal organoids.

2022-12-01 | GSE171395 | GEO

HNF4a acts as upstream functional regulator of intestinal Wnt3 and Paneth cell fate

Project description:HNF4a acts as upstream functional regulator of intestinal Wnt3 and Paneth cell fate

| PRJNA719384 | ENA

HNF4a acts as upstream functional regulator of intestinal Wnt3 and Paneth cell fate [RNA-seq]

Project description:HNF4a acts as upstream functional regulator of intestinal Wnt3 and Paneth cell fate [RNA-seq]

| PRJNA720420 | ENA

Metastasis of colon cancer requires Dickkopf-2 to generate cancer cells with Paneth cell properties

Project description:Metastasis is the leading cause of cancer-related mortality. Paneth cells provide stem cell niche factors in the homeostatic condition, but the underlying mechanisms of cancer stem cell niche development are unclear. Here we report that Dickkopf-2 (DKK2) is essential for Paneth-like cell generation during the metastasis of colon cancer. Splenic injection of DKK2-knockout (KO) cancer organoids into C57BL/6 mice resulted in a significant reduction of liver metastases compared to the control cancer organoids in spite of the presence of carcinogenic mutations in Apc, Kras and Tp53 genes. RNA-seq analysis of DKK2 KO organoids showed reduction of Paneth cell marker genes such as Lysozymes and Defensins. Ingenuity pathway analysis (IPA) of the RNA-seq data and assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) suggested HNF4A as a downstream target of DKK2. Chromatin immunoprecipitation followed by sequencing (Chip-seq) analysis showed that HNF4A binds to the open chromatin regions of Sox9, a well-known transcription factor for Paneth cell differentiation. Reduction of Paneth-like cells in the absence of DKK2 has been confirmed in the murine metastatic model of colon cancer using flow cytometry, immunohistochemistry and single cell RNA-seq. These data suggest the necessity of DKK2 in Paneth-like cell generation. Thus, DKK2 contributes to stem cell niche development during the metastatic progression of colon cancer.

2024-11-11 | GSE277510 | GEO

Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts

2010-11-29 | GSE25109 | GEO

Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts

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

HNF4α Acts as Upstream Functional Regulator of Intestinal Wnt3 and Paneth Cell Fate.

Project description:Background & aimsThe intestinal epithelium intrinsically renews itself ex vivo via the proliferation of Lgr5+ intestinal stem cells, which is sustained by the establishment of an epithelial stem cell niche. Differentiated Paneth cells are the main source of epithelial-derived niche factor supplies and produce Wnt3 as an essential factor in supporting Lgr5+ stem cell activity in the absence of redundant mesenchymal Wnts. Maturation of Paneth cells depends on canonical Wnt signaling, but few transcriptional regulators have been identified to this end. The role of HNF4α in intestinal epithelial cell differentiation is considered redundant with its paralog HNF4γ. However, it is unclear whether HNF4α alone controls intrinsic intestinal epithelial cell growth and fate in the absence of a mesenchymal niche.MethodsWe used transcriptomic analyses to dissect the role of HNF4α in the maintenance of jejunal epithelial culture when cultured ex vivo as enteroids in the presence or absence of compensatory mesenchymal cells.ResultsHNF4α plays a crucial role in supporting the growth and survival of jejunal enteroids. Transcriptomic analyses revealed an autonomous function of HNF4α in Wnt3 transcriptional regulation and Paneth cell differentiation. We showed that Wnt3a supplementation or co-culture with intestinal subepithelial mesenchymal cells reversed cell death and transcriptional changes caused by the deletion of Hnf4a in jejunal enteroids.ConclusionsOur results support the intrinsic epithelial role of HNF4α in regulating Paneth cell homeostasis and intestinal epithelium renewal in the absence of compensatory Wnt signaling.

| S-EPMC9871320 | biostudies-literature

Human small intestinal organoids grown with a specific protocol to enrich for Paneth cells were treated with an inhbitor (GSK-LSD1) for the epigenetic modulator LSD1.

Project description:To assess the role of LSD1 in human intestinal epithelium, human small intestinal organoids were treated with an inhibitor for LSD1 (GSK-LSD1) and compared to untreated organoids. The organoids were grown with specific conditions where Paneth cells are present in the organoids as similar experiments in mice show that Paneth cells disappear upon GSK-LSD1 treatment. Similar to mouse intestinal organoids, Paneth cells dissappear upon GSK-LSD1 treatment. Furthermore, we used these gene set enrichment analysis on these microarray data to show that these human intestinal organoids have a similar phenotype as mice epithelium without LSD1.

2020-11-16 | E-MTAB-7863 | biostudies-arrayexpress

Bulk RNA-seq of wild type, HNF4A-knockout (KO), HNF4G-KO, and HNF4A/4G-double KO (DKO) kidney organoids

Project description:We performed bulk RNA-seq and compared complehensive gene expression profiles of kidney organoids induced from wild type, HNF4A-KO, HNF4G-KO, and HNF4A/4G-DKO iPS cell lines.

2023-10-23 | GSE226439 | GEO

HNF4A

Project description:HNF4A

| PRJNA940175 | ENA