Expression profiling of gastric cancer samples by oligonucleotide microarray analysis reveals low degree of intra-tumor variability

作     者：Karolin Trautmann Christine Steudel Dana Grossmann Daniela Aust Gerhard Ehninger Stephan Miehike Christian Thiede 

作者机构：Medical Department Ⅰ Department of Pathology 

出 版 物：《World Journal of Gastroenterology》 (世界胃肠病学杂志（英文版）)

年 卷 期：2005年第11卷第38期

页      面：5993-5996页

核心收录：

学科分类：1002[医学-临床医学] 100214[医学-肿瘤学] 10[医学] 

基　　金：Supported by a MeDDrive grant From the University of Dresden 2003by a grant from the Dr. Mildred Scheel Stiftung No. 70-2923 

主　　题：胃癌 寡核苷酸 肿瘤活性 基因表达 病理机制 

摘      要：AIM: Gene expression profiling provides an unique opportunity to gain insight into the development of different types of gastric cancer. Tumor sample heterogeneity is thought to decrease the sensitivity and tumor specificity of microarray analysis. Thus, microdissection and preamplification of RNA is frequently performed. However, this technique may also induce considerable changes to the expression profile. To assess the effect of gastric tumor heterogeneity on expression profiling results, we measured the variation in gene expression within the same gastric cancer sample by performing a gene chip analysis with two RNA preparations extracted from the same tumor ***: Tumor samples from six intestinal T2 gastric tumors were dissected under liquid nitrogen and RNA was prepared from two separate tumor fragments. Each extraction was individually processed and hybridized to an Affymetrix U133A gene chip covering approximately 18 000 human gene transcripts. Expression profiles were analyzed using Microarray Suite 5.0 (Affymetrix) and GeneSpring 6.0 (Silicon Genetics).RESULTS: All gastric cancers showed little variance in expression profiles between different regions of the same tumor sample. In this case, gene chips displayed mean pair wise correlation coefficients of 0.94±0.02 (mean±SD),compared to values of 0.61±0.1 for different tumor samples. Expression of the variance between the two expression profiles as a percentage of total change (Affymetrix) revealed a remarkably low average value of 1.18±0.78 for comparing fragments of the same tumor *** contrast, comparison of fragments from different tumors revealed a percentage of 24.4±***: Our study indicates a low degree of expression profile variability within gastric tumor samples isolated from one patient. These data suggest that tumor tissue heterogeneity is not a dominant source of error for microarray analysis of larger tumor samples, making total RNA extraction an appropriate strategy