Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of lung cancer tumors from a female, non-smoking taiwanese population: Genome-wide screening of transcriptional modulation in non-smoking female lung cancer in Taiwan

ABSTRACT: Although smoking is the major risk factor for lung cancer, only 7% of female lung cancer patients in Taiwan have a history of cigarette smoking, extremely lower than those in Caucasian females. This report is a comprehensive analysis of the molecular signature of non-smoking female lung cancer in Taiwan. RNA was extracted from paired tumor and normal tissues for gene expression analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Tzu-Pin Lu

PROVIDER: E-GEOD-19804 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women.

Lu Tzu-Pin TP Tsai Mong-Hsun MH Lee Jang-Ming JM Hsu Chung-Ping CP Chen Pei-Chun PC Lin Chung-Wu CW Shih Jin-Yuan JY Yang Pan-Chyr PC Hsiao Chuhsing Kate CK Lai Liang-Chuan LC Chuang Eric Y EY

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 20100827 10

<h4>Background</h4>Although cigarette smoking is the major risk factor for lung cancer, only 7% of female lung cancer patients in Taiwan have a history of smoking. The genetic mechanisms of carcinogenesis in nonsmokers are unclear, but semaphorins have been suggested to play a role as lung tumor suppressors. This report is a comprehensive analysis of the molecular signature of nonsmoking female lung cancer patients in Taiwan, with a particular focus on the semaphorin gene family.<h4>Methods</h4> ...[more]

PMID: 20802022

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Project description:Tobacco smoking is responsible for over 90% of lung cancer cases, and yet the precise molecular alterations induced by smoking in lung that develop into cancer and impact survival have remained obscure. We performed gene expression analysis using HG-U133A Affymetrix chips on 135 fresh frozen tissue samples of adenocarcinoma and paired noninvolved lung tissue from current, former and never smokers, with biochemically validated smoking information. ANOVA analysis adjusted for potential confounders, multiple testing procedure, Gene Set Enrichment Analysis, and GO-functional classification were conducted for gene selection. Results were confirmed in independent adenocarcinoma and non-tumor tissues from two studies. We identified a gene expression signature characteristic of smoking that includes cell cycle genes, particularly those involved in the mitotic spindle formation (e.g., NEK2, TTK, PRC1). Expression of these genes strongly differentiated both smokers from non-smokers in lung tumors and early stage tumor tissue from non-tumor tissue (p<0.001 and fold-change>1.5, for each comparison), consistent with an important role for this pathway in lung carcinogenesis induced by smoking. These changes persisted many years after smoking cessation. NEK2 (p<0.001) and TTK (p=0.002) expression in the noninvolved lung tissue was also associated with a 3-fold increased risk of mortality from lung adenocarcinoma in smokers. Our work provides insight into the smoking-related mechanisms of lung neoplasia, and shows that the very mitotic genes known to be involved in cancer development are induced by smoking and affect survival. These genes are candidate targets for chemoprevention and treatment of lung cancer in smokers. Experiment Overall Design: Overall, 180 adenocarcinoma and non-tumor tissue samples were selected for the analyses, including duplicate or triplicate samples from 14 subjects for quality control. From the original 180 samples, 148 provided sufficient quantity of high-quality RNA for microarray analyses; 13 additional samples were excluded because of problematic assays. Normalization was conducted on the remaining 135 microarrays. After normalization, 13 samples were excluded because of low percentage of tumor cells in the tumor tissues. This report is based on 122 samples, of which 15 duplicates were averaged, resulting in 107 final expression values from 58 tumor and 49 non-tumor tissues from 20 never smokers, 26 former smokers, and 28 current smokers.

Dataset Information

Transcription profiling of lung cancer tumors from a female, non-smoking taiwanese population: Genome-wide screening of transcriptional modulation in non-smoking female lung cancer in Taiwan

Publications

Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women.

Similar Datasets

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