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MiRNA and lung cancer (INCA project) - 26 RNG25k microarrays

ABSTRACT: Gene expression analysis in 13 pairs of primary lung cancers and their corresponding non cancerous lung tissues. These specimens were obtained from the Nice Hospital Tumor Bio Bank, France. Dye swap-experiment comparing cancerous tissue versus adjacent normal lung tissue.

ORGANISM(S): Homo sapiens

SUBMITTER: Puisségur MP

PROVIDER: S-ECPF-GEOD-18694 | biostudies-other | 2011 Mar

REPOSITORIES: biostudies-other

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MiRNA and lung cancer (INCA project) - 26 RNG25k microarrays

Project description:Gene expression analysis in 13 pairs of primary lung cancers and their corresponding non cancerous lung tissues. These specimens were obtained from the Nice Hospital Tumor Bio Bank, France.

2010-10-01 | GSE18694 | GEO

MiRNA and lung cancer (INCA project) - 40 miRNAs microarrays

Project description:MicroRNA expression pattern in 20 pairs of primary lung cancers and their corresponding non cancerous lung tissues. These specimens were obtained from the Nice Hospital Tumor Bio Bank, France. Dye swap-experiment comparing cancerous tissue versus adjacent normal lung tissue.

| S-ECPF-GEOD-18692 | biostudies-other

MiRNA and lung cancer (INCA Project) - 16 RNG25k microarrays

Project description:To identify putative novel specific targets of mir-210, we overexpressed miR-210 as well as miR-34a and a siRNA targeted against E2F3 in A549 human adenocarcinoma cells by transfecting them with synthetic pre-miRNAs or a synthetic “negative” pre-miRNA as control (miR-Neg). RNA samples were harvested at 48 hours post-transfection and 2 independent experiments were carried out. 48 hours post-transfection, 2 independent experiments performed in dye-swap: miR-210 versus miR-Neg ; miR-34a versus miR-Neg ; si-E2F3 versus miR-Neg ; si-control versus miR-Neg.

| S-ECPF-GEOD-18695 | biostudies-other

MiRNA and lung cancer (INCA project) - 26 RNG25k microarrays

2010-09-30 | E-GEOD-18694 | biostudies-arrayexpress

MiRNA and lung cancer (INCA Project) - 16 RNG25k microarrays

2010-10-01 | GSE18695 | GEO

MiRNA and lung cancer (INCA project) - 40 miRNAs microarrays

2010-10-01 | GSE18692 | GEO

MiRNA and lung cancer (INCA project) - 40 miRNAs microarrays

2010-09-30 | E-GEOD-18692 | biostudies-arrayexpress

MiRNA and lung cancer (INCA Project) - 16 RNG25k microarrays

2010-09-30 | E-GEOD-18695 | biostudies-arrayexpress

The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease.

Project description:Recent studies have established that mutations or deletions in microRNA (miRNA) processing enzymes resulting in a global decrease of miRNA expression are frequent across cancers and can be associated with a poorer prognosis. While very popular in miRNA profiling studies, it remains unclear whether miRNA microarrays are suited or not to accurately detecting global miRNA decreases seen in cancers. In this work, we analyzed the miRNA profiles of samples with global miRNA decreases using Affymetrix miRNA microarrays following the inducible genetic deletion of Dicer1. Surprisingly, up to a third of deregulated miRNAs identified upon Dicer1 depletion were found to be up-regulated following standard robust multichip average (RMA) background correction and quantile normalization, indicative of normalization bias. Our comparisons of five preprocess steps performed at the probe level demonstrated that the use of cyclic loess relying on non-miRNA small RNAs present on the Affymetrix platform significantly improved specificity and sensitivity of detection of decreased miRNAs. These findings were validated in samples from patients with prostate cancer, where conjugation of robust normal-exponential background correction with cyclic loess normalization and array weights correctly identified the greatest number of decreased miRNAs, and the lowest amount of false-positive up-regulated miRNAs. These findings highlight the importance of miRNA microarray normalization for the detection of miRNAs that are truly differentially expressed and suggest that the use of cyclic loess based on non-miRNA small RNAs can help to improve the sensitivity and specificity of miRNA profiling in cancer samples with global miRNA decrease.

| S-EPMC3683922 | biostudies-literature

Smoking, Alcohol, and Biliary Tract Cancer Risk: A Pooling Project of 26 Prospective Studies.

Project description:BackgroundTobacco and alcohol are well-established risk factors for numerous cancers, yet their relationship to biliary tract cancers remains unclear.MethodsWe pooled data from 26 prospective studies to evaluate associations of cigarette smoking and alcohol consumption with biliary tract cancer risk. Study-specific hazard ratios (HRs) and 95% confidence intervals (CIs) for associations with smoking and alcohol consumption were calculated. Random-effects meta-analysis produced summary estimates. All statistical tests were two-sided.ResultsOver a period of 38 369 156 person-years of follow-up, 1391 gallbladder, 758 intrahepatic bile duct, 1208 extrahepatic bile duct, and 623 ampulla of Vater cancer cases were identified. Ever, former, and current smoking were associated with increased extrahepatic bile duct and ampulla of Vater cancers risk (eg, current vs never smokers HR = 1.69, 95% CI = 1.34 to 2.13 and 2.22, 95% CI = 1.69 to 2.92, respectively), with dose-response effects for smoking pack-years, duration, and intensity (all Ptrend < .01). Current smoking and smoking intensity were also associated with intrahepatic bile duct cancer (eg, >40 cigarettes per day vs never smokers HR = 2.15, 95 % CI = 1.15 to 4.00; Ptrend = .001). No convincing association was observed between smoking and gallbladder cancer. Alcohol consumption was only associated with intrahepatic bile duct cancer, with increased risk for individuals consuming five or more vs zero drinks per day (HR = 2.35, 95%CI = 1.46 to 3.78; Ptrend = .04). There was evidence of statistical heterogeneity among several cancer sites, particularly between gallbladder cancer and the other biliary tract cancers.ConclusionsSmoking appears to increase the risk of developing all biliary tract cancers except gallbladder cancer. Alcohol may increase the risk of intrahepatic bile duct cancer. Findings highlight etiologic heterogeneity across the biliary tract.

| S-EPMC6910180 | biostudies-literature

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