Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines

Abstract: BACKGROUND: The aim of this study was to characterize gene expression and DNA copy number profiles in androgen sensitive (AS) and androgen insensitive (AI) prostate cancer cell lines on a genome-wide scale. METHODS: Gene expression profiles and DNA copy number changes were examined using DNA microarrays in eight commonly used prostate cancer cell lines. Chromosomal regions with DNA copy number changes were identified using cluster along chromosome (CLAC). RESULTS: There were discrete differences in gene expression patterns between AS and AI cells that were not limited to androgen-responsive genes. AI cells displayed more DNA copy number changes, especially amplifications, than AS cells. The gene expression profiles of cell lines showed limited similarities to prostate tumors harvested at surgery. CONCLUSIONS: AS and AI cell lines are different in their transcriptional programs and degree of DNA copy number alterations. This dataset provides a context for the use of prostate cancer cell lines as models for clinical cancers. This SuperSeries is composed of the SubSeries listed below. Overall design: Refer to individual Series

摘要：
研究背景：本研究旨在在全基因组范围内解析雄激素敏感（androgen sensitive, AS）与雄激素不敏感（androgen insensitive, AI）前列腺癌细胞系的基因表达谱及DNA拷贝数特征。
研究方法：采用DNA微阵列（DNA microarrays）检测8种常用前列腺癌细胞系的基因表达谱与DNA拷贝数变异情况；通过染色体沿链聚类（cluster along chromosome, CLAC）算法鉴定存在DNA拷贝数变异的染色体区域。
研究结果：AS与AI细胞的基因表达模式存在显著差异，且该差异并非仅局限于雄激素应答基因；AI细胞的DNA拷贝数变异（尤其是拷贝数扩增事件）数量多于AS细胞；各细胞系的基因表达谱与手术切除获取的前列腺肿瘤组织的相似性较为有限。
研究结论：AS与AI细胞系在转录程序及DNA拷贝数变异程度上均存在差异。本数据集可为将前列腺癌细胞系作为临床肿瘤研究模型提供参照依据。本SuperSeries由下述SubSeries组成。整体设计：详见各系列说明。