Taniguchi Itsuki, Iwaya Chihiro, Ohnaka Keizo, Shibata Hiroki, Yamamoto Ken
Division of Genomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
Department of Geriatric Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
Hum Genomics. 2017 May 12;11(1):8. doi: 10.1186/s40246-017-0106-6.
Epidemiological studies of DNA methylation profiles may uncover the molecular mechanisms through which genetic and environmental factors contribute to the risk of multifactorial diseases. There are two types of commonly used DNA bioresources, peripheral blood cells (PBCs) and EBV-transformed lymphoblastoid cell lines (LCLs), which are available for genetic epidemiological studies. Therefore, to extend our knowledge of the difference in DNA methylation status between LCLs and PBCs is important in human population studies that use these DNA sources to elucidate the epigenetic risks for multifactorial diseases. We analyzed the methylation status of the autosomes for 192 and 92 DNA samples that were obtained from PBCs and LCLs, respectively, using a human methylation 450 K array. After excluding SNP-associated methylation sites and low-call sites, 400,240 sites were subjected to analysis using a generalized linear model with cell type, sex, and age as the independent variables.
We found that the large proportion of sites showed lower methylation levels in LCLs compared with PBCs, which is consistent with previous reports. We also found that significantly different methylation sites tend to be located on the outside of the CpG island and in a region relatively far from the transcription start site. Additionally, we observed that the methylation change of the sites in the low-CpG promoter region was remarkable. Finally, it was shown that the correlation between the chronological age and ageing-associated methylation sites in ELOVL2 and FHL2 in the LCLs was weaker than that in the PBCs.
The methylation levels of highly methylated sites of the low-CpG-density promoters in PBCs decreased in the LCLs, suggesting that the methylation sites located in low-CpG-density promoters could be sensitive to demethylation in LCLs. Despite being generated from a single cell type, LCLs may not always be a proxy for DNA from PBCs in studies of epigenome-wide analysis attempting to elucidate the role of epigenetic change in disease risks.
DNA甲基化谱的流行病学研究可能揭示遗传和环境因素导致多因素疾病风险的分子机制。遗传流行病学研究常用的两种DNA生物资源是外周血细胞（PBC）和EB病毒转化的淋巴母细胞系（LCL）。因此，在利用这些DNA来源阐明多因素疾病的表观遗传风险的人群研究中，扩展我们对LCL和PBC之间DNA甲基化状态差异的认识非常重要。我们使用人类甲基化450K芯片，分别分析了从PBC和LCL获得的192个和92个DNA样本的常染色体甲基化状态。在排除单核苷酸多态性（SNP）相关的甲基化位点和低信号位点后，以细胞类型、性别和年龄作为自变量，使用广义线性模型对400,240个位点进行分析。
我们发现，与PBC相比，LCL中大部分位点的甲基化水平较低，这与之前的报道一致。我们还发现，显著不同的甲基化位点往往位于CpG岛之外且相对远离转录起始位点的区域。此外，我们观察到低CpG启动子区域位点的甲基化变化显著。最后，结果表明，LCL中ELOVL2和FHL2的实际年龄与衰老相关甲基化位点之间的相关性比PBC中的弱。
PBC中低CpG密度启动子的高甲基化位点在LCL中的甲基化水平降低，这表明位于低CpG密度启动子中的甲基化位点可能对LCL中的去甲基化敏感。尽管LCL由单一细胞类型产生，但在试图阐明表观遗传变化在疾病风险中作用的全表观基因组分析研究中，LCL可能并不总是PBC DNA的替代物。
