Genome-wide DNA methylation analysis in canine gastrointestinal lymphoma
Genome-wide DNA methylation analysis in canine gastrointestinal lymphoma
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DOI：
10.1292/jvms.19-0547
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发表时间：
2020-05-01
影响因子：
1.2
通讯作者：
Takiguchi, Mitsuyoshi
中科院分区：
文献类型：
--
作者：
Ohta, Hiroshi;Yamazaki, Jumpei;Takiguchi, Mitsuyoshi
DNA甲基化是甲基基团对DNA的共价修饰，主要在CpG二核苷酸处，并且是研究最多的表观遗传机制之一，其导致基因表达变异性而不影响DNA序列。DNA甲基化的全基因组分析确定了可以定义人类淋巴瘤患者亚型的特征。本研究的目的是进行全基因组分析的DNA甲基化在狗胃肠道淋巴瘤（GIL）。从10只患有GIL的狗的内窥镜活检中提取基因组DNA。我们进行了DNA甲基化的数字限制性酶分析（DREAM），用于全基因组DNA甲基化分析，可以提供犬基因组中CpG位点DNA甲基化水平的高度定量信息。我们成功获得了每个GIL样本148，601 - 162，364个CpG位点的定量DNA甲基化水平数据。接下来，我们分析了83，132个CpG位点，以剖析GIL和正常外周血单核细胞（PBMC）之间DNA甲基化的差异。我们发现，与PBMC相比，GIL病例中有383- 3，054个CpG位点高度甲基化。有趣的是，包括61个基因的启动子区域在内的773个CpG位点在超过一半的病例中被鉴定为通常高甲基化，表明GIL中异常的保守DNA甲基化模式。本研究揭示了犬GIL中普遍存在大量的高甲基化位点。这些异常的DNA甲基化可能参与了犬GIL的肿瘤发生。
DNA methylation is the covalent modification of methyl groups to DNA mostly at CpG dinucleotides and one of the most studied epigenetic mechanisms that leads to gene expression variability without affecting the DNA sequence. Genome-wide analysis of DNA methylation identified the signatures that could define subtypes of human lymphoma patients. The objective of this study was to conduct the genome-wide analysis of DNA methylation in dogs with gastrointestinal lymphoma (GIL). Genomic DNA was extracted from endoscopic biopsies from 10 dogs with GIL. We performed Digital Restriction Enzyme Assay of DNA Methylation (DREAM) for genome-wide DNA methylation analysis that could provide highly quantitative information on DNA methylation levels of CpG sites across the dog genome. We successfully obtained data of quantitative DNA methylation level for 148,601-162,364 CpG sites per GIL sample. Next, we analyzed 83,132 CpG sites to dissect the differences in DNA methylation between GIL and normal peripheral blood mononuclear cells (PBMCs). We found 383-3,054 CpG sites that were hypermethylated in GIL cases compared to PBMCs. Interestingly, 773 CpG sites including promoter regions of 61 genes were identified to be commonly hypermethylated in more than half of the cases, suggesting conserved DNA methylation patterns that are abnormal in GIL. This study revealed that there was a large number of hypermethylated sites that are common in most of canine GIL. These abnormal DNA methylation could be involved in tumorigenesis of the canine GIL.