Identification of genes with a correlation between copy number and expression in gastric cancer

BMC Medical Genomics

Qinghua Zhang²  Hengjun Gao²  Huasheng Xiao²  Wen Zhang²  Qing Zhang¹  Yanqing Yang⁴  Sheng Yang⁴  Ping Wang³  Lei Cheng² 

[1] Department of Oncology, Gongli Hospital, Shanghai, China;National Engineering Center for Biochip at Shanghai, Shanghai, China;Department of Pathology, Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China;State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China

关键词: Gastric cancer;    Biomarkers;    Correlation;    Gene expression profile;    Copy number variations;   

Others  :  1134917
DOI  :  10.1186/1755-8794-5-14

 received in 2011-12-10, accepted in 2012-03-27,  发布年份 2012

【 摘 要 】

Background

To elucidate gene expression associated with copy number changes, we performed a genome-wide copy number and expression microarray analysis of 25 pairs of gastric tissues.

Methods

We applied laser capture microdissection (LCM) to obtain samples for microarray experiments and profiled DNA copy number and gene expression using 244K CGH Microarray and Human Exon 1.0 ST Microarray.

Results

Obviously, gain at 8q was detected at the highest frequency (70%) and 20q at the second (63%). We also identified molecular genetic divergences for different TNM-stages or histological subtypes of gastric cancers. Interestingly, the C20orf11 amplification and gain at 20q13.33 almost separated moderately differentiated (MD) gastric cancers from poorly differentiated (PD) type. A set of 163 genes showing the correlations between gene copy number and expression was selected and the identified genes were able to discriminate matched adjacent noncancerous samples from gastric cancer samples in an unsupervised two-way hierarchical clustering. Quantitative RT-PCR analysis for 4 genes (C20orf11, XPO5, PUF60, and PLOD3) of the 163 genes validated the microarray results. Notably, some candidate genes (MCM4 and YWHAZ) and its adjacent genes such as PRKDC, UBE2V2, ANKRD46, ZNF706, and GRHL2, were concordantly deregulated by genomic aberrations.

Conclusions

Taken together, our results reveal diverse chromosomal region alterations for different TNM-stages or histological subtypes of gastric cancers, which is helpful in researching clinicopathological classification, and highlight several interesting genes as potential biomarkers for gastric cancer.

【 授权许可】

   
2012 Cheng et al.; licensee BioMed Central Ltd.

【 图 表 】

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