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Expression data from mouse intestinal organoids I

ABSTRACT: APC inactivation is the early process in the tumorigenesis of colorectal cancer. We established organoid cultures from intestines of genetically modifeid mice harboring Apcfl/fl and R26CreERT2 allele We used microarrays to determine the alterations in intestinal stem cells in response to APC inactivation.

ORGANISM(S): Mus musculus

PROVIDER: GSE76847 | GEO | 2016/03/31

SECONDARY ACCESSION(S): PRJNA308752

REPOSITORIES: GEO

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Expression data from mouse intestinal organoids II

Project description:APC inactivation is the early process in the tumorigenesis of colorectal cancer. We established organoid cultures from intestines of genetically modifeid mice harboring Apcfl/fl, Tacc3wt/wt or Apcfl/fl, Tacc3fl/fll and R26CreERT2 allele We used microarrays to determine the alterations in intestinal stem cells in response to Tacc3 disruption.

2016-04-30 | GSE76848 | GEO

Expression data from mouse intestinal organoids I

Project description:APC inactivation is the early process in the tumorigenesis of colorectal cancer. We established organoid cultures from intestines of genetically modifeid mice harboring Apcfl/fl and R26CreERT2 allele We used microarrays to determine the alterations in intestinal stem cells in response to APC inactivation. Organoids were treated with 4OHT to induce recombination of APC or left untreated, and collected at 4 or 6 days after treatment. RNA were extracted and hybridization on Affymetrix microarrays.

2016-03-31 | E-GEOD-76847 | biostudies-arrayexpress

Lipid Profiling of Mouse Intestinal Organoids for studying APC Mutations

Project description:Inactivating mutations including both germline and somatic mutations in the adenomatous polyposis coli (APC) gene drives most familial and sporadic colorectal cancers. Understanding the metabolic implications of this mutation will aid to establish its wider impact on cellular behaviour and potentially inform clinical decisions. However, to date, alterations in lipid metabolism induced by APC mutations remain unclear. Intestinal organoids have gained widespread popularity in studying colorectal cancer and chemotherapies, because their three-dimensional structure more accurately mimics an in vivo environment. Here, we aimed to investigate intra-cellular lipid disturbances induced by APC gene mutations in intestinal organoids using a reversed-phase ultra-high-performance liquid chromatography mass spectrometry (RP-UHPLC-MS)-based lipid profiling method. Lipids of the organoids grown from either wildtype (WT) or mice with Apc mutations (Lgr5–EGFP-IRES-CreERT2 Apcfl/fl) were extracted and analysed using RP-UHPLC-MS. Concentrations of phospholipids (e.g. PC(16:0/16:0), PC(18:1/20:0), PC(38:0), PC(18:1/22:1)), ceramides (e.g. Cer(d18:0/22:0), Cer(d42:0), Cer(d18:1/24:1)) and hexosylceramide (e.g. HexCer(d18:1/16:0), HexCer(d18:1/22:0)) were higher in Apcfl/fl organoids, whereas levels of sphingomyelins (e.g. SM(d18:1/14:0), SM(d18:1/16:0) ) were lower compared to WT. These observations indicate that cellular metabolism of sphingomyelin was upregulated, resulting in the cellular accumulation of ceramides and production of HexCer due to the absence of Apcfl/fl in the organoids. Our observations demonstrated lipid profiling of organoids and provided an enhanced insight into the effects of the APC mutations on lipid metabolism, making for a valuable addition to screening options of the organoid lipidome.

2021-02-17 | ST001707 | MetabolomicsWorkbench

Characterization of gastric tumor organoids with specific oncogenic pathway activations

Project description:Gastric cancer ranks the fifth most common malignancy and the third leading cause of cancer related death worldwide. Classical chemotherapy is still the standard treatment in advanced stages, with only two targeted therapies currently in clinical use. Several targeted trials have failed, likely due to missing relevant biomarkers that predict response. Patient derived cancer organoids (PDOs) constitute a three dimensional cell culture system showing self renewal, self organization and regularly unlimited proliferation while faithfully recapitulating many aspects of the tumor they are derived from. Nevertheless, the complex individual mutational landscape hampers the use of PDOs for basic and translational research. We therefore characterized three murine tumor organoid models with defined mutational patterns altering specific oncogenic pathways: a RAS activated (KrasG12D, Tp53R172H), a WNT activated (Apcfl/fl, Tp53R172H) and a diffuse (Cdh1fl/fl, Apcfl/fl) tumor model. The models were analyzed phenotypically, a proteome signature was established and a drug screen performed. The models were morphologically diverse, were characterized by individual protein expression signatures and showed differential drug sensitivities. The developed organoid models allow functional assays as well as pathway specific drug interference testing in a genetically defined setting.

2022-08-22 | PXD022015 | Pride

Transcription profiling by array of Apc-deficient mouse small intestinal epithelium upon Msx1 depletion.

Project description:The first step in the development of human colorectal cancer is the aberrant hyperactivation of the Wnt signaling pathway, predominantly caused by inactivating mutations in the adenomatous polyposis coli (Apc) gene encoding an essential tumor suppressor. The gene encoding transcriptional factor msh homeobox 1 (Msx1) displayed robust upregulation upon Apc inactivation in intestinal epithelium isolated in mice harboring the conditional allele of the Apc gene. To identify the gene signature in the small intestine upon Msx1 depletion, small intestinal epithelium from mice harboring conditional alleles of Apc and Msx1 was isolated and the gene expression profile was compared with control mice harboring the conditional allele of Apc only.

2019-11-01 | E-MTAB-6930 | biostudies-arrayexpress

Transcriptomes of intestinal blood endothelial cells (BEC) from mice with acute epithelial Apc deletion.

Project description:APC is mutated in the majority of colorectal cancers. Inducible deletion of Apc in intestinal epithelial cells in Apcfl//fl; Villin-CreERT2 mice recapitulates this tumor-initiating mutation resulting in expanded intestinal crypts, including stem cells. We used microarrays to analyze BEC gene expression changes during the early stages of intestinal tumorigenesis.

2022-03-29 | GSE111783 | GEO

RAC-GEF function as a critical factor in intestinal tumourigenesis

Project description:VilCreER APCfl/fl vs VilCreER APCfl/fl, Vav2-/-, Vav3-/-, Tiam1-/-

| PRJEB25520 | ENA

RNA-seq of mouse intestinal organoids treated with interferon-gamma

Project description:We aimed to investigate gene expression changes in intestinal organoids from different mouse genotypes after treatment with interferon-gamma. Wild-type, villinCreER;KrasG12D/+;Trp53fl/flRosa26N1icd/+ (KPN), and villinCreER;Apcfl/fl;KrasG12D/+;Trp53fl/flTgfbrIfl/fl (AKPT) intestinal organoids were plated, and the media was supplemented with 1 ng/mL of recombinant mouse interferon-gamma protein on Day 3. RNA was collected 24h later and processed for RNA sequencing.

2022-06-30 | E-MTAB-11769 | biostudies-arrayexpress

RNA-seq of mouse intestinal organoids treated with TGF-beta

Project description:We aimed to investigate gene expression changes in intestinal organoids from different mouse genotypes after treatment with TGF-beta. Wild-type, villinCreER;KrasG12D/+;Trp53fl/flRosa26N1icd/+ (KPN), and villinCreER;Apcfl/fl;KrasG12D/+;Trp53fl/flTgfbrIfl/fl (AKPT) intestinal organoids were plated, and the media was supplemented with 5ng/mL of recombinant mouse TGFß1 protein on Day 3. RNA was collected 24h later and processed for RNA sequencing.

2022-06-30 | E-MTAB-11784 | biostudies-arrayexpress

Gene expression profiels from organoids.

Project description:Recent studies have suggested increased plasticity of differentiated cells within the intestine to act both as intestinal stem cells and tumour initiating cells. However, little is known of the processes that regulate this plasticity. Our previous work has shown that activating mutations of Kras or the NF-kB pathway can drive dedifferentiation of intestinal cells lacking Apc. To investigate this process further, we profiled organoids by gene expression analysis. Organoids were isolated from VillinCreER Apcfl/fl KrasG12D crypts (here called CC) or Villi (here called SFV).

2017-06-13 | GSE99100 | GEO

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