Identification of novel human Wnt target genes using adult endodermal tissue-derived organoids
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PROVIDER: PRJNA703016 | ENA |
REPOSITORIES: ENA
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Project description:WNT and/or Rspondin was withdrawn from the medium and Wnt pathway inhibitors IWP2 and DKK1 were added to the growth medium of human stomach, liver, pancreas, small intestinal and colon organoids and RNA was harvested at time points 0h, 6h and 24h to identify Wnt regulated genes.
2021-02-22 | GSE167115 | GEO
Project description:Constitutive Wnt activation upon loss of Adenoma polyposis coli (APC) acts as main driver of colorectal cancers (CRC). Targeting Wnt signaling has proven difficult because the pathway is crucial for homeostasis and stem cell renewal. To distinguish oncogenic from physiologic Wnt activity, we have performed transcriptome and proteome profiling in isogenic human colon organoids. Culture in the presence or absence of exogenous ligand allowed us to discriminate receptor-mediated signaling from the effects of CRISPR/Cas9 induced APC loss. We could catalogue two non-overlapping molecular signatures that were stable at distinct levels of stimulation. Newly identified markers for normal stem/progenitor cells and adenomas were validated by immunohistochemistry and flow cytometry. We found that oncogenic Wnt signals are associated with good prognosis in tumors of the consensus molecular subtype 2 (CMS2). In contrast, receptor-mediated signaling was linked to CMS4 tumors and poor prognosis. Together, our data represent a valuable resource for biomarkers that allow more precise stratification of Wnt responses in CRC.
2019-02-28 | PXD012650 | Pride
Project description:Based on the ability of FGF and/or WNT signaling to control posterior fate and intestinal lineage commitment, several groups have reported that treating mouse or human Pluripotent Stem Cell (PSC) derived definitive endoderm (DE) with small molecules or ligands that activate WNT signaling, or a combination of WNT and FGF signaling can induce an intestinal fate in human DE. In this current study, we leverage hESC derived human intestinal organoids (HIOs) to test the hypothesis that the duration of exposure to high levels of FGF and WNT signaling controls regional intestinal identity, with shorter durations generating intestine similar to the proximal duodenum, and longer durations distalizing HIOs to become similar to jejunum/ileum. Our results demonstrate that exposing human definitive endoderm (DE) cultures to short or long incubations of media that activate WNT and FGF siganling results in gene and protein expression profiles that are consistent with tissue that has been patterned into proximal (duodenum) or distal (ileum) small intestine, respectively.
2016-07-04 | E-MTAB-4168 | biostudies-arrayexpress
Project description:The Wnt target gene Lgr5 marks actively dividing stem cells in Wnt-driven, self-renewing tissues such as small intestine and colon, stomach and hair follicles. A 3D culture system allows long-term clonal expansion of single Lgr5+ stem cells into transplantable organoids that retain many characteristics of the original epithelial architecture. A crucial component of the culture medium is the Wnt agonist Rspo, the recently discovered ligand of Lgr5. Here we show that Lgr5-LacZ is not expressed in healthy adult liver, yet that small Lgr5-LacZ+ cells appear near bile ducts upon damage, coinciding with robust activation of Wnt signaling. As shown by lineage tracing using a novel Lgr5-ires-CreERT2 knock-in allele, damage-induced Lgr5+ cells generate hepatocytes and bile ducts in vivo. Single Lgr5+ cells from damaged liver can be clonally expanded as organoids in Rspo1-based culture medium over multiple months. Such clonal organoids can be induced to differentiate in vitro and to generate functional hepatocytes upon transplantation into FAH-/- mice. These findings imply that previous findings on Lgr5+ stem cells in actively self-renewing tissues extend to damage-induced stem cells in a tissue with a low rate of spontaneous self-renewal. We first generated arrays from multiple wildtype tissues including muscle, white adipose tissues, brown adipose tissues, liver and pancreas. Then we generated arrays from liver derived cultures maintained in different conditions, and compared the expression profile with the corresponding parental tissues and other non-related tissues.
2013-01-28 | E-GEOD-32210 | biostudies-arrayexpress
Project description:Regeneration capacity of intestinal epithelial cells are highly dependent on the status of stemness. In the homeostasis, only a small subset of stem cells is responsible for the turnover of the intestinal epithelium. However, at the injury, such as caused by radiation, intestinal epithelial cells show substantial plasticity for regeneration. Most of the colorectal cancers (CRCs) are differentiated adenocarcinoma, which maintain the expression of both stemness and differentiation markers, suggesting an existence of a similar regeneration system as in normal cells, although the role of such fluctuation of stemness in regeneration of cancer after irradiation is not well understood. In the present study, we first examined the effect of radiation on growth, stemness and differentiation using organoids derived from differentiated CRC. Both proliferation and stemness markers were once drastically decreased after sub-lethal dose of irradiation, meanwhile differentiation markers remained. After the static phase, regrowth foci consisting of proliferating cells with expression of the stem cell markers reappeared. We applied the foci formation to a radio-sensitivity assay in CRC organoids. Radio-sensitivity, the ability of foci formation, differed among the examined lines, and correlated well with the in vivo radiation sensitivity. The radio-sensitivity decreased after mechanical disruption of the organoids, which we have reported to increase the stemness of CRC organoids in a WNT dependent manner. Pre-treatment of organoids with histone deacetylase inhibitors increased radiation sensitivity, accompanied with suppressed expression of WNT target genes, and WNT inhibitors increased radio-sensitivity, suggesting that not all but some of the cancer cells with high WNT activity at the timing of radiation is the origin of the foci formation. The radiation sensitivity assay using CRC organoids established in the present study would provide a novel platform to evaluate the radiosensitizers against differentiated adenocarcinoma of CRC.
2019-11-07 | GSE139995 | GEO
Project description:ChIP-seq was performed to determine the transcriptional activity of genes during endodermal differentiation RNA pol II occupancy and histone marks of elongation and gene repression were analyzed during early endodermal differentiation
2012-09-25 | E-GEOD-41111 | biostudies-arrayexpress
Project description:Constitutive Wnt activation upon loss of Adenoma polyposis coli (APC) acts as main driver of colorectal cancers (CRC). Targeting Wnt signaling has proven difficult because the pathway is crucial for homeostasis and stem cell renewal. To distinguish oncogenic from physiologic Wnt activity, we have performed comprehensive transcriptome and proteome profiling in human colon organoids. Culture in the presence or absence of exogenous ligand allowed us to discriminate receptor-mediated signaling from the effects of CRISPR/Cas9 induced APC loss. We could catalogue two non-overlapping molecular signatures that were stable at distinct levels of stimulation. Newly identified markers for normal colon stem/progenitor cells and adenomas were validated by immunohistochemistry and flow cytometry. We found that oncogenic Wnt signals are associated with good prognosis in tumors of the consensus molecular subtype 2 (CMS2). In contrast, receptor-mediated signaling was linked to CMS4 tumors and poor prognosis. Together, our data represent a valuable resource for biomarkers that allow more precise stratification of Wnt responses in CRC.
2019-02-11 | GSE125472 | GEO
Project description:scRNAseq of primary fetal liver (6 post conceptional weeks), fetal biliary organoids, hepatoblast organoids, hepatoblast organoids after withdrawl of Wnt and transfer to hepatozyme medium, hepatoblast organoids after TGFb treatment.
2022-05-04 | E-MTAB-7189 | biostudies-arrayexpress
Project description:Constitutive Wnt activation upon loss of Adenoma polyposis coli (APC) acts as main driver of colorectal cancers (CRC). Targeting Wnt signaling has proven difficult because the pathway is crucial for homeostasis and stem cell renewal. To distinguish oncogenic from physiologic Wnt activity, we have performed comprehensive transcriptome and proteome profiling in human colon organoids. Culture in the presence or absence of exogenous ligand allowed us to discriminate receptor-mediated signaling from the effects of CRISPR/Cas9 induced APC loss. We could catalogue two non-overlapping molecular signatures that were stable at distinct levels of stimulation. Newly identified markers for normal colon stem/progenitor cells and adenomas were validated by immunohistochemistry and flow cytometry. We found that oncogenic Wnt signals are associated with good prognosis in tumors of the consensus molecular subtype 2 (CMS2). In contrast, receptor-mediated signaling was linked to CMS4 tumors and poor prognosis. Together, our data represent a valuable resource for biomarkers that allow more precise stratification of Wnt responses in CRC.
2019-02-11 | GSE125578 | GEO
Project description:Human colon organoids reveal distinct physiologic and oncogenic Wnt responses
| PRJNA516452 | ENA