Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors

Genomic DNA copy number alterations are key genetic events in the development and progression of human cancers. Here we report a genome-wide microarray comparative genomic hybridization (array CGH) analysis of DNA copy number variation in a series of primary human breast tumors. We have profiled DNA copy number alteration across 6,691 mapped human genes, in 44 predominantly advanced, primary breast tumors and 10 breast cancer cell lines. While the overall patterns of DNA amplification and deletion corroborate previous cytogenetic studies, the high-resolution (gene-by-gene) mapping of amplicon boundaries and the quantitative analysis of amplicon shape provide significant improvement in the localization of candidate oncogenes. Parallel microarray measurements of mRNA levels reveal the remarkable degree to which variation in gene copy number contributes to variation in gene expression in tumor cells. Specifically, we find that 62% of highly amplified genes show moderately or highly elevated expression, that DNA copy number influences gene expression across a wide range of DNA copy number alterations (deletion, low-, mid- and high-level amplification), that on average, a 2-fold change in DNA copy number is associated with a corresponding 1.5-fold change in mRNA levels, and that overall, at least 12% of all the variation in gene expression among the breast tumors is directly attributable to underlying variation in gene copy number. These findings provide evidence that widespread DNA copy number alteration can lead directly to global deregulation of gene expression, which may contribute to the development or progression of cancer.

基因组DNA拷贝数改变（Genomic DNA copy number alterations）是人类癌症发生与进展进程中的关键遗传事件。本研究针对一系列原发性人类乳腺肿瘤，开展了全基因组微阵列比较基因组杂交（array CGH）分析，以检测DNA拷贝数变异情况。我们对44例以进展期原发性乳腺肿瘤为主的样本以及10株乳腺癌细胞系中共计6691个已定位的人类基因的DNA拷贝数改变情况进行了图谱分析。尽管DNA扩增与缺失的整体模式与既往细胞遗传学研究结果一致，但本研究通过高分辨率（逐基因）定位扩增子（amplicon）边界，并对扩增子形态进行定量分析，显著提升了候选癌基因（candidate oncogenes）的定位精度。同步开展的mRNA水平微阵列检测结果显示，基因拷贝数变异对肿瘤细胞内基因表达变异的影响程度十分显著。具体而言，本研究发现：62%的高扩增基因呈现中等或高度上调的表达水平；DNA拷贝数可在缺失、低水平、中水平及高水平扩增等广泛的DNA拷贝数改变类型范围内影响基因表达；平均而言，DNA拷贝数每发生2倍变化，对应mRNA水平便会出现1.5倍的相应变化；整体来看，乳腺肿瘤样本中至少12%的基因表达变异可直接归因于基因拷贝数的固有变异。上述研究结果证实，广泛存在的DNA拷贝数改变可直接引发基因表达的全局失调，这或许会推动癌症的发生与进展。