Center of Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, United States of America.
PLoS One. 2010 Sep 29;5(9):e13020. doi: 10.1371/journal.pone.0013020.
Follicular lymphoma (FL) is a form of non-Hodgkin's lymphoma (NHL) that arises from germinal center (GC) B-cells. Despite the significant advances in immunotherapy, FL is still not curable. Beyond transcriptional profiling and genomics datasets, there currently is no epigenome-scale dataset or integrative biology approach that can adequately model this disease and therefore identify novel mechanisms and targets for successful prevention and treatment of FL.
METHODOLOGY/PRINCIPAL FINDINGS: We performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19(+) B-cells using 454 sequencing technology. The methylated DNA fragments were enriched with methyl-binding proteins, treated with bisulfite, and sequenced using the Roche-454 GS FLX sequencer. The total number of bases covered in the human genome was 18.2 and 49.3 million including 726,003 and 1.3 million CpGs in FL and CD19(+) B-cells, respectively. 11,971 and 7,882 methylated regions of interest (MRIs) were identified respectively. The genome-wide distribution of these MRIs displayed significant differences between FL and normal B-cells. A reverse trend in the distribution of MRIs between the promoter and the gene body was observed in FL and CD19(+) B-cells. The MRIs identified in FL cells also correlated well with transcriptomic data and ChIP-on-Chip analyses of genome-wide histone modifications such as tri-methyl-H3K27, and tri-methyl-H3K4, indicating a concerted epigenetic alteration in FL cells.
CONCLUSIONS/SIGNIFICANCE: This study is the first to provide a large scale and comprehensive analysis of the DNA methylation sequence composition and distribution in the FL epigenome. These integrated approaches have led to the discovery of novel and frequent targets of aberrant epigenetic alterations. The genome-wide bisulfite sequencing approach developed here can be a useful tool for profiling DNA methylation in clinical samples.
滤泡性淋巴瘤（FL）是一种起源于生发中心（GC）B 细胞的非霍奇金淋巴瘤（NHL）。尽管免疫疗法取得了重大进展，但 FL 仍然无法治愈。除了转录谱和基因组数据集外，目前还没有全基因组范围的表观基因组数据集或综合生物学方法可以充分模拟这种疾病，从而确定新的机制和靶点，以成功预防和治疗 FL。
方法/主要发现：我们使用 454 测序技术对 FL 细胞和正常 CD19(+)B 细胞进行了甲基化富集全基因组亚硫酸氢盐测序。用甲基结合蛋白富集甲基化 DNA 片段，用亚硫酸氢盐处理，然后用罗氏 454 GS FLX 测序仪进行测序。人类基因组中覆盖的碱基总数为 18.2 和 49.3 百万，分别包括 FL 和 CD19(+)B 细胞中的 726,003 和 1.3 万个 CpG。分别鉴定了 11,971 和 7,882 个感兴趣的甲基化区域（MRIs）。这些 MRI 在 FL 和正常 B 细胞之间的全基因组分布存在显著差异。在 FL 和 CD19(+)B 细胞中观察到 MRI 在启动子和基因体之间的分布呈反向趋势。FL 细胞中鉴定的 MRI 也与转录组数据和全基因组组蛋白修饰的 ChIP-on-Chip 分析（如三甲基-H3K27 和三甲基-H3K4）很好地相关，表明 FL 细胞中存在协同的表观遗传改变。
结论/意义：本研究首次提供了 FL 表观基因组中 DNA 甲基化序列组成和分布的大规模综合分析。这些综合方法导致发现了新的和频繁的异常表观遗传改变靶标。这里开发的全基因组亚硫酸氢盐测序方法可以成为分析临床样本中 DNA 甲基化的有用工具。
