Trautmann Karolin, Steudel Christine, Grossmann Dana, Aust Daniela, Ehninger Gerhard, Miehlke Stephan, Thiede Christian
Medical Department I, Fetscherstr. 74, 01307 Dresden, Germany.
World J Gastroenterol. 2005 Oct 14;11(38):5993-6. doi: 10.3748/wjg.v11.i38.5993.
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 pre-amplification 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 specimen.
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).
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 sample. In contrast, comparison of fragments from different tumors revealed a percentage of 24.4+/-4.5.
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 for performing gene chip expression profiling of gastric cancer.
基因表达谱分析为深入了解不同类型胃癌的发展提供了独特契机。肿瘤样本的异质性被认为会降低微阵列分析的敏感性和肿瘤特异性。因此，经常进行RNA的显微切割和预扩增。然而，该技术也可能对表达谱产生相当大的改变。为评估胃肿瘤异质性对表达谱分析结果的影响，我们通过对从同一肿瘤标本中提取的两种RNA制剂进行基因芯片分析，测量了同一胃癌样本内基因表达的差异。
在液氮下解剖6例肠型T2胃癌的肿瘤样本，并从两个单独的肿瘤片段中制备RNA。每次提取均单独处理，并与覆盖约18000个人类基因转录本的Affymetrix U133A基因芯片杂交。使用微阵列套件5.0（Affymetrix）和基因弹簧6.0（硅基因公司）分析表达谱。
所有胃癌在同一肿瘤样本的不同区域之间，表达谱差异很小。在这种情况下，基因芯片显示平均成对相关系数为0.94±0.02（平均值±标准差），而不同肿瘤样本的值为0.61±0.1。将两个表达谱之间的差异表达作为“总变化”（Affymetrix）的百分比，对于同一肿瘤样本片段的比较，平均值得出的显著低值为1.18±0.78。相比之下，不同肿瘤片段的比较显示百分比为24.4±4.5。
我们的研究表明，从一名患者分离的胃肿瘤样本中，表达谱变异性程度较低。这些数据表明，肿瘤组织异质性不是大肿瘤样本微阵列分析误差的主要来源，使得总RNA提取成为进行胃癌基因芯片表达谱分析的合适策略。
