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Characterization of microRNA expression in colorectal cancer

ABSTRACT: MiRNAs have differential expression between normal colon and cancer tissues, and could be targets for CRC therapies and be further developed as potential diagnostic and prognostic analytes. Keywords: classification 66 samples from 49 patients

ORGANISM(S): Homo sapiens

SUBMITTER: Jack Yu

PROVIDER: E-GEOD-10259 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Characterization of global microRNA expression reveals oncogenic potential of miR-145 in metastatic colorectal cancer.

Arndt Greg M GM Dossey Lesley L Cullen Lara M LM Lai Angela A Druker Riki R Eisbacher Michael M Zhang Chunyan C Tran Nham N Fan Hongtao H Retzlaff Kathy K Bittner Anton A Raponi Mitch M

BMC cancer 20091020

<h4>Background</h4>MicroRNAs (MiRNAs) are short non-coding RNAs that control protein expression through various mechanisms. Their altered expression has been shown to be associated with various cancers. The aim of this study was to profile miRNA expression in colorectal cancer (CRC) and to analyze the function of specific miRNAs in CRC cells. MirVana miRNA Bioarrays were used to determine the miRNA expression profile in eight CRC cell line models, 45 human CRC samples of different stages, and fo ...[more]

PMID: 19843336

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Characterization of microRNA expression in colorectal cancer

Project description:MiRNAs have differential expression between normal colon and cancer tissues, and could be targets for CRC therapies and be further developed as potential diagnostic and prognostic analytes. Keywords: classification

2009-03-20 | GSE10259 | GEO

Transcriptome profiling in advanced colorectal cancer

Project description:In total, 89 samples were collected from 89 patients with colorectal cancer (CRC), of which 66 patients had stage IV CRC. We sequenced the mRNAs purified from the formalin-fixed paraffin embedded (FFPE) blocks.

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Expression profiles of colorectal cancer cell lines

Project description:We ortho-topically implanted 16 human colorectal cancer (CRC) cell lines onto the cecal walls of nude mice . To identify the genes possibly involved in EMT of CRC, we analyze the EMT related changes with the orthotopic implantation method in vivo in combination with that of gene expression profiles using a cDNA microarray in vitro. We analyzed 16 human colorectal cancer cell lines. For each cell line, the experiments were carried out twice.

2013-09-01 | E-GEOD-49811 | biostudies-arrayexpress

Colorectal cancer classification based on gene expression is not associated with FOLFIRI response

Project description:Sadanandam et al. (2013) recently published a study based on the use of microarray data to classify colorectal cancer (CRC) samples. The classification claimed to have strong clinical implications, as reflected in the paper title: “A colorectal cancer classification system that associates cellular phenotype and responses to therapy”. They defined five subtypes: (i) inflammatory; (ii) goblet-like; (iii) enterocyte; (iv) transit-amplifying; and (v) stem-like. Based on drug sensitivity data from 21 patients, they also reported that the so-called stem-like subtype show differential sensitivity to FOLFIRI. This is the key result in their publication, since it implies a direct relation between the subtype and the choice of CRC therapy (i.e. FOLFIRI response). However, our analyses using the same drug sensitivity data and results from additional patients showed that the CRC classification reported by Sadanandam et al. is not predictive of FOLFIRI response. We used the classification algorithm to obtain CRC subtypes from our samples. Then we tested the subtype-drug response association performing a retrospective study.

2014-09-10 | E-GEOD-54483 | biostudies-arrayexpress

Expression data from human colonic biopsy sample

Project description:Gene expression profile based classification of colonic diseases are suitable for identification of diagnostic mRNA expression patterns which can establish the basis of a new molecular biological diagnostic method Keywords: whole genomic expression Total RNA was extracted from colonic biosy samples CRC and hybridized on Affymetrix HGU133 Plus 2.0 microarrays

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Epigenomic Analysis of Aberrantly Methylated Genes in Colorectal Cancer

Project description:Determination of the profile of genes commonly aberrantly methylated in colorectal cancer (CRC) has substantial potential value for diagnostic and therapeutic application. However, our knowledge of the DNA methylation pattern in CRC is currently limited. Therefore, we analyzed the methylation profile of 27,578 CpG sites spanning more than 14,000 genes in CRC and in adjacent normal mucosa using beadchip array-based technology. We identified 621 CpG sites located in promoter region and CpG islands that were significantly hypermethylated in CRC compared to normal mucosa. Genes on chromosome 18 showed promoter hypermethylation most frequently. According to gene ontology analysis, the most common biologically relevant class of genes affected by methylation was the class associated with the cadherin signaling pathway. In comparison with genome-wide expression array, mRNA expression was more like to be down-regulated in the genes demonstrating promoter hypermethylation, although this was not statistically significant. We validated 10 CpG sites that were shown to be hypermethylated in the array studies (ADHFE1, BOLL, SLC6A15, ADAMTS5, TFPI2, EYA4, NPY, TWIST1, LAMA1, GAS7) and 2 CpG sites showing hypomethylaion (MAEL, SFT2D3) in CRC compared to normal mucosa using pyrosequencing. The methylation status measured by pyrosequencing was consistent with the methylation array data. In conclusion, we have shown that methylation profiling based on beadchip arrays is an effective method for screening for aberrantly methylated genes in CRC. In addition, we identified novel methylated genes that are candidate diagnostic or prognostic markers for CRC. We measured the methylation status of the 27,578 CpG sites (Human Methylation27 DNA Analysis BeadChip) in 22 pairs of CRC tissue and adjacent normal mucosa to identify genes that are commonly aberrantly methylated in CRC.

2010-06-24 | E-GEOD-17648 | biostudies-arrayexpress

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2015-12-15 | ST000284 | MetabolomicsWorkbench

Classification of serrated colorectal tumors

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2006-07-28 | GSE4045 | GEO

Consensus Molecular Subtype predicts differential vulnerability of colorectal cancer to the survivin suppressant YM155 I

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C. elegans: wildtype vs nhr-49-/-; wildtype vs nhr-66-/-; wildtype vs nhr-80-/-

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