GEO DataSets

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

30 Samples

Download data: CSV

(Submitter supplied) Wnt signaling plays a pivotal role in colorectal cancer. Intrinsic activation of Wnt by mutational events, such as mutations in the tumor suppressor gene APC, represents the most frequent initiating event in this disease background. Long truncated versions of APC retain partial functionality, which leads to a sub-maximal, “just right” activation state of Wnt signaling supposed to be beneficial for disease initiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) AP4 is frequently expressed in primary CRCs. However, the in vivo relevance of AP4 for development of intestinal tumor formation has not been analyzed by genetic approaches. ApcMin/+ mice with deletion of AP4 were generated and analyzed. The mRNA expression profiles of intestinal adenomas with and without functional AP4 were compared.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) AP4 is frequently expressed in primary CRCs. However, the in vivo relevance of AP4 for development of intestinal tumor formation has not been analyzed by genetic approaches. ApcMin/+ mice with deletion of AP4 were generated and analyzed. The mRNA expression profiles of intestinal adenomas with and without functional AP4 were compared.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) mRNA expression from tubular adenomas of patients with Familial Adenomatous Polyposis

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: TXT

(Submitter supplied) Traditional serrated adenomas (TSAs) are rare colorectal polyps characterized by unique histology features. Fusions in R-spondin genes have been found in TSAs, but it is not clear whether these are sufficient for TSA development. We established 2 patient-derived TSA organoid lines, and engineered chromosome rearrangements that involve R-spondin genes into human colonic organoids using CRISPR-Cas9. Consequently, we highlighted the similarity of the gene expression patterns between TSA organoids and engineered organoids.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

6 Samples

Download data: CEL

(Submitter supplied) Using 5' droplet-based single cell sequencing, we profiled single cells dervied from human colorectal cancer organoids carrying either APC mutation or RSPO fusion, and paired normal colon organoids for the later.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) To develop a better understanding of the biology underlying risk for CRC posed by germ line APC mutations we performed DNA methylation analysis of colon organoids derived from normal-appearing colons of FAP subjects (n=7) and matched healthy individuals (n=16). We identified a large number (n=358) of differentially methylated regions (DMRs) between colon organoids of FAP and healthy subjects, many of which were also identified in a comparison of tumor and normal adjacent tissue (NAT) in two independent, sporadic CRC tumor cohorts.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

23 Samples

Download data: CSV, IDAT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL10558 GPL570

28 Samples

Download data: CEL

(Submitter supplied) Resistance to Ras pathway inhibition is a major challenge in the treatment of colorectal cancer (CRC), but the underlying mechanisms are incompletely understood. Here we performed large-scale small molecule screens in CRC and identified inhibitors of MEK1/2 as potent activators of Wnt/beta-catenin signalling. Targeting MEK increased Wnt activity in different CRC cell lines and in the murine intestine in vivo. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL

(Submitter supplied) Resistance to Ras pathway inhibition is a major challenge in the treatment of colorectal cancer (CRC), but the underlying mechanisms are incompletely understood. Here we performed large-scale small molecule screens in CRC and identified inhibitors of MEK1/2 as potent activators of Wnt/beta-catenin signalling. Targeting MEK increased Wnt activity in different CRC cell lines and in the murine intestine in vivo. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

24 Samples

Download data: TXT

(Submitter supplied) To asses the effect of Apc loss on the intestinal epithelium we induced homozygous VillinCreERT2 Apc flox/flox mice with tamoxifen on 3 consecutive days (day 0, 1 and 2), and harvested small intestinal epithelium on day 3.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

8 Samples

Download data: IDAT, TXT

(Submitter supplied) To assess cellular changes upon abrogation of the WNT-signaling pathway, we induced expression of a dominant-negative T-cell factor 4 (TCF4). This showed a remarkable overlap with activation of the unfolded protein response (UTR) in the same colon cancer cell line.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

6 Samples

Download data

(Submitter supplied) To assess the effect of activation of the unfolded protein response (UPR) in colon cancer cell lines, we treated cells with the AB5 subtilase cytotoxin (SubAB). This proteolytically cleaves the 78-kDa glucose-regulated protein (GRP78; also known as HSPA5 or BiP) inside the endoplasmic reticulum. We find that the WNT signaling pathway is highly affected upon treatment with SubAB.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

6 Samples

Download data

(Submitter supplied) A key function of Na+/H+ exchanger regulatory factor 2 (NHERF2) is spatial organization of signaling proteins to facilitate signal transduction. The role of NHERF2 in cancer progress is not well understood. This study determines how loss of NHERF2 alter colon cancer progress.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: TAR, TXT

(Submitter supplied) APC mutant mice develop polys in the intestine, but not carcinoma. We found that additional deletion of Olfm4 gene induced carcinoma formation in the distal colon. To explore the molecular mechanism, we performed cDNA microarray to understand the gene expression files in the tumor tissues compared with WT, APC mutant and Olfm4 mutant mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

15 Samples

Download data: CEL

(Submitter supplied) Almost all colorectal cancers (CRC) present with mutations in the Apc gene, leading to unrestrained Wnt activation and the initiation of tumour development. We previously reported the competitive benefit of Apc-mutant intestinal stem cells (ISCs) within the crypt, however, the mechanism by which they outcompete their wild type (WT) neighbours remained elusive. Here, we studied the effect of Apc-mutants using an in vitro culture system of WT (Lgr5-CreErt2) and Apc-/- (Lgr5-CreErt2;Apcfl/fl) organoids . more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL17021

16 Samples

Download data: TXT

(Submitter supplied) BRAFV600E confers poor prognosis and a distinct molecular type of colorectal cancer, which is often associated with TP53 alterations. In order to understand how BRAFV600E and p53R172H promote tumorigenesis in the intestinal epithelium, we generated murine organoids harboring conditional BraffloxV600E and/or Trp53LSL-R172H alleles and conducted RNA sequencing analysis after sudden oncogene induction. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

24 Samples

Download data: TXT

(Submitter supplied) In this experiment, we determined the differences in the transcriptomes of freshly isolated murine small intestine and colon derived crypts. The data shows that the mRNA profiles of the two tissues significantly differ in their ground state. Interestingly, we found that the expression levels of ERK pathway components as well as their positive and negative regulators significantly differ between small intestinal and colonic crypts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: TXT