Shi Huidong, Guo Juyuan, Duff Deiter J, Rahmatpanah Farahnaz, Chitima-Matsiga Rebecca, Al-Kuhlani Mufadhal, Taylor Kristen H, Sjahputera Ozy, Andreski Melinda, Wooldridge James E, Caldwell Charles W
Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, MO 65203, USA.
Carcinogenesis. 2007 Jan;28(1):60-70. doi: 10.1093/carcin/bgl092. Epub 2006 Jun 14.
Non-Hodgkin's lymphoma (NHL) is a group of malignancies with heterogeneous genetic and epigenetic alterations. Discovery of molecular markers that better define NHL should improve diagnosis, prognosis and understanding of the biology. We developed a CpG island DNA microarray for discovery of aberrant methylation targets in cancer, and now apply this method to examine NHL cell lines and primary tumors. This methylation profiling revealed differential patterns in six cell lines originating from different subtypes of NHL. We identified 30 hypermethylated genes in these cell lines and independently confirmed 10 of them. Methylation of 6 of these genes was then further examined in 75 primary NHL specimens composed of four subtypes representing different stages of maturation. Each gene (DLC-1, PCDHGB7, CYP27B1, EFNA5, CCND1 and RARbeta2) was frequently hypermethylated in these NHLs (87, 78, 61, 53, 40 and 38%, respectively), but not in benign follicular hyperplasia. Although some genes such as DLC-1 and PCDHGB7 were methylated in the vast majority of NHLs, others were differentially methylated in specific subtypes. The methylation of the candidate tumor suppressor gene DLC-1 was detected in a high proportion of primary tumor and plasma DNA samples by using quantitative methylation-specific PCR analysis. This promoter hypermethylation inversely correlated with DLC-1 gene expression in primary NHL samples. Thus, this CpG island microarray is a powerful discovery tool to identify novel methylated genes for further studies of their relevant molecular pathways in NHLs and identification of potential epigenetic biomarkers of disease.
非霍奇金淋巴瘤（NHL）是一组具有异质性基因和表观遗传改变的恶性肿瘤。发现能更好地定义NHL的分子标志物应可改善诊断、预后并增进对其生物学特性的理解。我们开发了一种用于发现癌症中异常甲基化靶点的CpG岛DNA微阵列，现在将此方法应用于检测NHL细胞系和原发性肿瘤。这种甲基化谱分析揭示了源自NHL不同亚型的6种细胞系中的差异模式。我们在这些细胞系中鉴定出30个高甲基化基因，并独立验证了其中10个。然后在由代表不同成熟阶段的四种亚型组成的75例原发性NHL标本中进一步检测了其中6个基因的甲基化情况。每个基因（DLC-1、PCDHGB7、CYP27B1、EFNA5、CCND1和RARbeta2）在这些NHL中均频繁出现高甲基化（分别为87%、78%、61%、53%、40%和38%），但在良性滤泡性增生中未出现。尽管某些基因如DLC-1和PCDHGB7在绝大多数NHL中发生甲基化，但其他基因在特定亚型中存在差异甲基化。通过定量甲基化特异性PCR分析在高比例的原发性肿瘤和血浆DNA样本中检测到候选抑癌基因DLC-1的甲基化。这种启动子高甲基化与原发性NHL样本中DLC-1基因表达呈负相关。因此，这种CpG岛微阵列是一种强大的发现工具，可用于鉴定新的甲基化基因，以进一步研究其在NHL中的相关分子途径并鉴定潜在的疾病表观遗传生物标志物。
