Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

MRNA and miRNA expression profiles for fresh frozen periampullary adenocarcinomas (pancreatobiliary and intestinal type) and adjacent normal tissues. [mRNA]

ABSTRACT: To study the molecular signatures of mRNAs and miRNAs which can potentially act as a prognostic biomarkers in pancreatobiliary and intestinal types of periampullary adenocarcinomas Total RNA was isolated from 10 x 20 Âµm sections of 81 fresh frozen tumor samples for mRNA expression profiling. A total of 49 PDAC, 8 bile duct adenocarcinoma, 8 ampulla of pancreatobiliary tye, 7 ampulla of intestinal type, 9 duodenum sample and 12 adjacent normal samples were used. These samples were analysed by microarray analysis using the 60K agilent platform. The expression profiles were background corrected and quantile normalized for mRNA. Filtering of controls, unannotated genes and low expressed probes was done.

ORGANISM(S): Homo sapiens

SUBMITTER: Vandana Sandhu

PROVIDER: E-GEOD-60979 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Molecular signatures of mRNAs and miRNAs as prognostic biomarkers in pancreatobiliary and intestinal types of periampullary adenocarcinomas.

Sandhu V V Bowitz Lothe I M IM Labori K J KJ Lingjærde O C OC Buanes T T Dalsgaard A M AM Skrede M L ML Hamfjord J J Haaland T T Eide T J TJ Børresen-Dale A-L AL Ikdahl T T Kure E H EH

Molecular oncology 20141219 4

Periampullary adenocarcinomas include four anatomical sites of origin (the pancreatic duct, bile duct, ampulla and duodenum) and most of them fall into two histological subgroups (pancreatobiliary and intestinal). Determining the exact origin of the tumor is sometimes difficult, due to overlapping histopathological characteristics. The prognosis depends on the histological subtype, as well as on the anatomical site of origin, the former being the more important. The molecular basis for these dif ...[more]

PMID: 25579086

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Project description:Transcription signatures have been used to stratify breast cancer patients into clinically distinct subgroups. However, transcription alone does not determine protein expression. Of potentially equal importance for determining the tumor phenotype is the rate at which transcripts are translated to form protein. Protein translation is controlled to a major degree by miRNA, and cancer cells may deregulate the expression of key genes by altering the activity of relevant miRNAs. The importance of miRNA deregulation and the extent to which multiple miRNAs coordinately deregulate key proteins in breast cancer is only partly understood. To gain such insight, we analyzed genome-wide miRNA expression and mRNA/protein expression for a panel of 105 selected cancer related genes in breast carcinomas from 283 patients. The miRNA-mRNA-protein interactome for the selected genes was constructed by modeling protein expression as a joint function of mRNA and miRNA expression, considering the effect of both one miRNA at a time, and all studied miRNAs simultaneously. The interactome represents a map of the global effects of miRNAs on protein expression, capturing direct as well as indirect effects. The results reveal extensive association between miRNA and protein expression as well as coordinated effects of multiple miRNAs on individual proteins. Applying the model onto two other independent primary breast cancer cohorts confirmed the generalizability of key aspects of the interactome map. The mRNA expression profiling of 283 breast cancer samples was performed using the SurePrint G3 Human GE 8x60K one-color microarrays from Agilent (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, v.6.5, May 2010). For each sample, 100 ng of RNA was amplified and hybridized on the array. Scanning was performed with Agilent Scanner G2565A, using AgilentG3_GX_1Color as profile. Signals were extracted using FE v.10.7.3.1 and protocol GE1_107_Sep09 (Agilent Technologies). Arrays were log2-transformed, quantile normalized and hospital-adjusted by subtracting from each probe value the mean probe value among samples from the same hospital. The Oslo Breast Cancer Consortium (OSBREAC)

Dataset Information

MRNA and miRNA expression profiles for fresh frozen periampullary adenocarcinomas (pancreatobiliary and intestinal type) and adjacent normal tissues. [mRNA]

Publications

Molecular signatures of mRNAs and miRNAs as prognostic biomarkers in pancreatobiliary and intestinal types of periampullary adenocarcinomas.

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