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Expression data from human colonic biopsy samples (adenoma-carcinoma)

ABSTRACT: Whole genomic microarray analysis was performed in order to identify gene expression profile alterations focusing on the dysplastic adenoma-carcinoma transition. Our aims were to determinate characteristic transcript sets for developing diagnostic mRNA expression patterns for objective classification of benign and malignant colorectal diseases and to test the classificatory power of these markers on an independent sample set.

ORGANISM(S): Homo sapiens

PROVIDER: GSE37364 | GEO | 2013/01/01

SECONDARY ACCESSION(S): PRJNA159563

REPOSITORIES: GEO

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Expression data from human colonic biopsy samples (adenoma-carcinoma)

Project description:Whole genomic microarray analysis was performed in order to identify gene expression profile alterations focusing on the dysplastic adenoma-carcinoma transition. Our aims were to determinate characteristic transcript sets for developing diagnostic mRNA expression patterns for objective classification of benign and malignant colorectal diseases and to test the classificatory power of these markers on an independent sample set. Total RNA was extracted from colonic biopsy samples of histologically negative patients and of patients with adenoma or colorectal cancer and were hybridized on Affymetrix HGU133 Plus 2.0 microarrays

2013-01-01 | E-GEOD-37364 | biostudies-arrayexpress

Colonic adenoma and adjacent normal single-cell RNA-seq

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

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miRNA experiment of fresh frozen colonic biopsy samples

Project description:The aim of the present study was to perform an additional global miRNA microarray analysis of tubular and tubulovillous adenoma biopsy specimen completed with colorectal adenocarcinomas using fresh frozen tisse

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Gene expression profiling in colonic adenoma and carcinoma in situ

Project description:The majority of colon carcinomas are known to develop in tubular adenomas through multi-stage carcinogenesis. Recently, we have reported a simple and reproducible method for the expression profiling using microdissected cells from formalin-fixed tissue samples (Lee et al, World J Gastroenterol, 11:1937-1945, 2005). Using the method, we analyzed the expression profiling in colon tubular adenoma/carcinoma sequence. Epithelial cells of carcinoma, tubular adenoma, and normal colon mucosa were microdissected from colon tubular adenomas containing focal adenocarcinomas. Keywords: disease (colon cancer) state analysis

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Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature

Project description:Background and Aims: Gene expression analysis of colon biopsies using high-density oligonucleotide microarray can contribute to the understanding of local pathophysiological alterations and to functional classification of precancerous adenoma, different stage colorectal carcinomas (CRC) and inflammatory bowel diseases (IBD). Results: Significant overexpression of collagen IV, lipocalin-2, caveolin-1, calumenin genes, and significant dowregulation of aquaporin-8, amnionless homolog, prostaglandin D2 receptor genes were detected in CRC patients compared to normal. Adenoma samples were characterized by upregulated CD44 antigen, met proto-oncogene and downregulated chemokine ligand-12, ADAM-like decysin-1 and ATP-binding casette A8 discriminatory genes. In IBD samples significantly increased lipocalin-2, interferon induced transmembrane protein 1 and 3 mRNA levels, decreased zinc finger protein 91 and transient receptor potential cation channel M6 mRNA levels were found. Ulcerative colitis and Crohn’s disease can be distinguished according to the top five genes: cyclin-G2; tripartite motif-containing-31; TNFR shedding aminopeptidase regulator-1; C-type lectin superfamily member-14 and AMICA. 88.3-97.8% of the cases was correctly classified according to discriminatory genes. Conclusions: Our whole genomic microarray analysis of biopsy samples provides discriminative signatures, and an insight into pathophysiological background of colonic diseases. The results afford a data warehouse which can be further mined for in-depth pathway analyses. Keywords: Colon biopsy specimens in diseased and normal state

2007-10-31 | GSE4183 | GEO

mRNA expression data from adenoma, gene modified, and colorectal cancer organoid.

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Identification of an intermediate signature that marks the initial phases of colorectal adenoma-carcinoma transition

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2022-01-12 | GSE179895 | GEO

Proteomic analysis of Hepatocellular Adenoma

Project description:Hepatocellular adenomas (HCA) are rare benign tumors that constitute a heterogeneous entity, divided into 5 groups based on molecular features (1) H-HCA with inactivating mutations of Hepatocyte Nuclear Factor 1A (HNF1α), (2) inflammatory HCA (IHCA) with diverse mutations activating the JAK/STAT pathway, (3) b-HCA with activating β-catenin mutation (4) recently identified sh-HCA presenting a Sonic Hedgehog pathway activation and finally, (5) the unclassified HCA (UHCA)). Risk of bleeding of sh-HCA and UHCA is their main clinical feature with malignant transformation. Nowadays, no specific biomarker exists to evaluate this hemorrhage risk. The objective of this study was to combine laser microdissection and mass spectrometry analysis to define Hepatocellular Adenoma proteome in the purpose of identifying specific biomarkers able to predict this bleeding risk.

2018-03-14 | PXD005571 | Pride

Human Transcriptome Array 2.0 (HTA) from healthy colonic, colorectal adenoma and colorectal cancer tissue

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