Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America.
PLoS Genet. 2012;8(6):e1002781. doi: 10.1371/journal.pgen.1002781. Epub 2012 Jun 21.
We have developed an enhanced form of reduced representation bisulfite sequencing with extended genomic coverage, which resulted in greater capture of DNA methylation information of regions lying outside of traditional CpG islands. Applying this method to primary human bone marrow specimens from patients with Acute Myelogeneous Leukemia (AML), we demonstrated that genetically distinct AML subtypes display diametrically opposed DNA methylation patterns. As compared to normal controls, we observed widespread hypermethylation in IDH mutant AMLs, preferentially targeting promoter regions and CpG islands neighboring the transcription start sites of genes. In contrast, AMLs harboring translocations affecting the MLL gene displayed extensive loss of methylation of an almost mutually exclusive set of CpGs, which instead affected introns and distal intergenic CpG islands and shores. When analyzed in conjunction with gene expression profiles, it became apparent that these specific patterns of DNA methylation result in differing roles in gene expression regulation. However, despite this subtype-specific DNA methylation patterning, a much smaller set of CpG sites are consistently affected in both AML subtypes. Most CpG sites in this common core of aberrantly methylated CpGs were hypermethylated in both AML subtypes. Therefore, aberrant DNA methylation patterns in AML do not occur in a stereotypical manner but rather are highly specific and associated with specific driving genetic lesions.
我们开发了一种增强型简化重亚硫酸盐测序方法，具有扩展的基因组覆盖范围，从而能够更全面地捕获位于传统 CpG 岛之外的 DNA 甲基化信息。将该方法应用于急性髓性白血病 (AML) 患者的原代人骨髓标本，我们发现遗传上不同的 AML 亚型表现出截然相反的 DNA 甲基化模式。与正常对照相比，我们观察到 IDH 突变型 AML 中广泛的超甲基化，优先靶向基因启动子区域和转录起始位点附近的 CpG 岛。相比之下，携带影响 MLL 基因的易位的 AML 表现出几乎完全排他性的 CpG 广泛去甲基化，而这些 CpG 则影响内含子和远端基因间 CpG 岛和岸区。与基因表达谱分析相结合，这些特定的 DNA 甲基化模式在基因表达调控中发挥了不同的作用。然而，尽管存在这种亚型特异性的 DNA 甲基化模式，但在两种 AML 亚型中，只有一小部分 CpG 位点始终受到影响。在这个异常甲基化 CpG 的共同核心中，大多数 CpG 位点在两种 AML 亚型中均呈超甲基化状态。因此，AML 中的异常 DNA 甲基化模式并非以刻板的方式发生，而是高度特异性的，并与特定的驱动遗传病变相关。
