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Differential gene expression in Lrig1null duodenal tumors compared to normal duodenum

ABSTRACT: Leucine-rich repeats and immunoglobulin-like domains 1 (Lrig1) is a pan-ErbB negative regulator and intestinal stem cell marker downregulated in many malignancies. Over 91% Lrig1-CreERT2/CreERT2 (Lrig1-/-) mice developed duodenal adenomas, providing the first in vivo evidence Lrig1 acts as a tumor suppressor. We thus characterize the differential expressing transcripts in these duodenal adenomas to explore the pathegenesis. Elevated expression of the Egfr ligands was detected in adenomas compared to adjacent normal tissue. These adenomas also expressed the gastric-specific genes Gastrokine1 and Mucin5ac, indicating gastric metaplasia. In this dataset, we include the expression data obtained from proximal adenomas as well as adjacent normal tissue and wildtype proximal duodenum. These data are used to obtain 679 upregulated and 874 downregulated transcripts in tumors.

ORGANISM(S): Mus musculus

PROVIDER: GSE64640 | GEO | 2015/01/04

SECONDARY ACCESSION(S): PRJNA271500

REPOSITORIES: GEO

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Differential gene expression in Lrig1null duodenal tumors compared to normal duodenum

Project description:Leucine-rich repeats and immunoglobulin-like domains 1 (Lrig1) is a pan-ErbB negative regulator and intestinal stem cell marker downregulated in many malignancies. Over 91% Lrig1-CreERT2/CreERT2 (Lrig1-/-) mice developed duodenal adenomas, providing the first in vivo evidence Lrig1 acts as a tumor suppressor. We thus characterize the differential expressing transcripts in these duodenal adenomas to explore the pathegenesis. Elevated expression of the Egfr ligands was detected in adenomas compared to adjacent normal tissue. These adenomas also expressed the gastric-specific genes Gastrokine1 and Mucin5ac, indicating gastric metaplasia. In this dataset, we include the expression data obtained from proximal adenomas as well as adjacent normal tissue and wildtype proximal duodenum. These data are used to obtain 679 upregulated and 874 downregulated transcripts in tumors. Total RNA from matched duodenal tumors or adjacent normal or wildtype duodenum was isolated with Rneasy (with Dnase digestion) and used to probe the Affymetrix Mouse Gene 1.0 ST chip; the probe was prepared with Ambion Expression Target preparation Kit P/N 4411974.

2015-01-04 | E-GEOD-64640 | biostudies-arrayexpress

Colonic adenoma and adjacent normal single-cell RNA-seq

Project description:colonic adenoma and adjacent normal from Lrig1-creERT2;Apc-fl/+ mouse

2018-10-23 | GSE117615 | GEO

Transcription profiling of mouse Rb1 deficient Apc1638N cecal tumors vs duodenal tumors

Project description:To examine the role of Rb1 in gastrointestinal (GI) tumors we generated mice with an Apc1638N allele, Rbtm2brn floxed alleles, and a villlin-cre transgene (RBVCA). These mice had reduced median survival due to an increase in tumor incidence and multiplicity in the cecum and the proximal colon; they differed from murine intestinal tumors of the Apc1638N type which normally arise solely in the small intestine. We have examined by micro-array analysis three cecal tumors from these mice (probable adenomas), and compared them to three duodenal tumors (probable adenocarcinomas). Expression profiles of duodenal and cecal tumors relative to each other show unique gene subsets up and down regulated. The two tumor types were subsequently shown to differentially regulate distinct sets of genes over expressed in a majority of human colorectal carcinomas. Experiment Overall Design: We have compared 3 cecal tumors with 3 duodenal tumors from Rb1 deficient Apc1638N mice.

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PIGA mutation and glycosylphosphatidylinositol anchor dysregulation in polyposis-associated duodenal tumorigenesis

Project description:Progression of duodenal polyposis into cancer is an important cause of morbidity and mortality in the inherited tumour syndromes Familial Adenomatous Polyposis (FAP) and MUTYH-associated Polyposis (MAP), yet this process remains poorly understood. This study aimed to identify genes that are mutated in FAP and MAP duodenal adenomas and to characterise the cellular consequences for duodenal tumorigenesis.

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mRNA profiling of AGS Gastric Cancer cell line treated with the Homeopathy formulation, Ornithogalum

Project description:Ornithogalum is one of the therapeutic formulation used in homeopathic treatments. It is specifically used in the treatment for gastric and duodenal ulcerations. Towards understanding the anticancer mechanism, we investigated the genome-wide mRNA changes upon treating AGS Gastric Cancer cells with Ornithogalum. We observed that totally 707 genes were significantly regulated upon Ornithogalum Treatment, among them 246 genes were upregulated and 461 genes were downregulated. The results provide insight into molecular implication and gene level expression of AGS upon treatment with Ornithogalum. Total RNA was isolated from AGS gastric cancer cells treated with 0.01% of ornithogalum and ethanol control and profiled using Affymetrix Human Gene 1.0 ST Array (HuGene-1_0-st).

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Genomic profiling of gastric adenomas by array-based comparative genomic hybridization

Project description:In this study, we investigated CNAs of 20 gastric CIS (Vienna category 4.2) and 20 adenomas, including 7 low-grade adenomas (LGA; Vienna category 3) and 13 high-grade adenomas (HGA; Vienna category 4.1), by 244k oligonucleotide-based array comparative genomic hybridization (array CGH). 20 gastric adenomas vs. 20 controls. The supplementary file 'GSE19574_aberrations.txt' file contains a summary of the aberrations in the gastric adenomas as determined by the ADM-2 algorithm.

2010-06-18 | E-GEOD-19574 | biostudies-arrayexpress

mRNA profiling of AGS Gastric Cancer cell line treated with the Homeopathy formulation, Ornithogalum

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Project description:To investigate transcriptomic differences between Cushing's disease adenomas and adjacent normal tissues We performed RNAseq analysis on CD adenomas versus their adjacent normal tissues

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Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution

Project description:Somatic L1 retrotransposition events have been shown to occur in epithelial cancers1-8. Here, we attempted to determine how early somatic L1 insertions occurred during the development of gastrointestinal (GI) cancers. Using L1-targeted resequencing (L1-seq), we studied different stages of four colorectal cancers arising from colonic polyps, seven pancreatic carcinomas, as well as seven gastric cancers. Surprisingly, we found somatic L1 insertions not only in all cancer types and metastases, but also in colonic adenomas, well-known cancer precursors. Some insertions were also present in low quantities in normal GI tissues, occasionally caught in the act of being clonally fixed in the adjacent tumors. Insertions in adenomas and cancers numbered in the hundreds and many were present in multiple tumor sections implying clonal distribution. Our results demonstrate that extensive somatic insertional mutagenesis occurs very early during the development of GI tumors, probably before dysplastic growth. We assessed the impact of somatic L1 insertions on the expression of the corresponding protein-coding genes by comparing protein abundance in the polyp with the highest number of somatic L1 insertions with that of its paired normal colon using mass spectrometry analysis. Of the 10 validated somatic insertions that were in protein coding regions in the polyp, two proteins – KIAA1217 and WARS2 – were downregulated in the adenoma >90% and >70%, respectively.

2015-08-11 | PXD001626 | Pride

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