Sadikovic Bekim, Yoshimoto Maisa, Al-Romaih Khaldoun, Maire Georges, Zielenska Maria, Squire Jeremy A
Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.
PLoS One. 2008 Jul 30;3(7):e2834. doi: 10.1371/journal.pone.0002834.
Genetic and epigenetic changes contribute to deregulation of gene expression and development of human cancer. Changes in DNA methylation are key epigenetic factors regulating gene expression and genomic stability. Recent progress in microarray technologies resulted in developments of high resolution platforms for profiling of genetic, epigenetic and gene expression changes. OS is a pediatric bone tumor with characteristically high level of numerical and structural chromosomal changes. Furthermore, little is known about DNA methylation changes in OS. Our objective was to develop an integrative approach for analysis of high-resolution epigenomic, genomic, and gene expression profiles in order to identify functional epi/genomic differences between OS cell lines and normal human osteoblasts. A combination of Affymetrix Promoter Tilling Arrays for DNA methylation, Agilent array-CGH platform for genomic imbalance and Affymetrix Gene 1.0 platform for gene expression analysis was used. As a result, an integrative high-resolution approach for interrogation of genome-wide tumour-specific changes in DNA methylation was developed. This approach was used to provide the first genomic DNA methylation maps, and to identify and validate genes with aberrant DNA methylation in OS cell lines. This first integrative analysis of global cancer-related changes in DNA methylation, genomic imbalance, and gene expression has provided comprehensive evidence of the cumulative roles of epigenetic and genetic mechanisms in deregulation of gene expression networks.
遗传和表观遗传变化导致基因表达失调和人类癌症的发生。DNA甲基化的变化是调节基因表达和基因组稳定性的关键表观遗传因素。微阵列技术的最新进展推动了用于分析遗传、表观遗传和基因表达变化的高分辨率平台的发展。骨肉瘤是一种儿童骨肿瘤，其特征是染色体数目和结构变化水平较高。此外，人们对骨肉瘤中的DNA甲基化变化知之甚少。我们的目标是开发一种综合方法，用于分析高分辨率的表观基因组、基因组和基因表达谱，以识别骨肉瘤细胞系与正常人成骨细胞之间的功能性表观/基因组差异。我们使用了Affymetrix启动子tiling阵列进行DNA甲基化分析、安捷伦阵列比较基因组杂交平台进行基因组失衡分析以及Affymetrix Gene 1.0平台进行基因表达分析。结果，开发出了一种用于探究全基因组肿瘤特异性DNA甲基化变化的综合高分辨率方法。该方法用于绘制首张基因组DNA甲基化图谱，并识别和验证骨肉瘤细胞系中DNA甲基化异常的基因。首次对DNA甲基化、基因组失衡和基因表达的全球癌症相关变化进行的综合分析，为表观遗传和遗传机制在基因表达网络失调中的累积作用提供了全面证据。
