Division of Advanced Preventive Medical Sciences, Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Sakamoto 1-12-4, Nagasaki, 852-8523, Japan.
Division of Advanced Preventive Medical Sciences and Leading Medical Research Core Unit, Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Sakamoto 1-12-4, Nagasaki, 852-8523, Japan.
J Hum Genet. 2022 Dec;67(12):711-720. doi: 10.1038/s10038-022-01083-4. Epub 2022 Sep 27.
Kabuki syndrome (KS) is a congenital malformation syndrome caused by mutations in the KMT2D and KDM6A genes that encode histone modification enzymes. Although KS is considered a single gene disorder, its symptoms vary widely. Recently, disease-specific DNA methylation patterns, or episignatures, have been recognized and used as a diagnostic tool for KS. Because of various crosstalk mechanisms between histone modifications and DNA methylation, DNA methylation analysis may have high potential for investigations into the pathogenesis of KS.
In this study, we investigated altered CpG-methylation sites that were specific to KS to find important genes associated with the various phenotypes or pathogenesis of KS. Whole genome bisulfite sequencing (WGBS) was performed to select target CpG islands, and enzymatic conversion technology was applied after hybridization capture to confirm KS-specific episignatures of 130 selected differently methylated target regions (DMTRs) in DNA samples from the 65 participants, 31 patients with KS and 34 unaffected individuals, in this study. We identified 26 candidate genes in 22 DMTRs that may be associated with KS. Our results indicate that disease-specific methylation sites can be identified from a small number of WGBS samples, and hybridization capture followed by enzymatic methylation sequencing can simultaneously test the sites.
Although DNA methylation can be tissue-specific, our results suggest that methylation profiling of DNA extracted from peripheral blood may be a powerful approach to study the pathogenesis of diseases.
歌舞伎综合征（KS）是一种先天性畸形综合征，由编码组蛋白修饰酶的 KMT2D 和 KDM6A 基因突变引起。尽管 KS 被认为是一种单基因疾病，但它的症状差异很大。最近，已识别出疾病特异性的 DNA 甲基化模式，或外显子签名，并将其用作 KS 的诊断工具。由于组蛋白修饰和 DNA 甲基化之间存在各种串扰机制，因此 DNA 甲基化分析可能对 KS 发病机制的研究具有很高的潜力。
在这项研究中，我们研究了特定于 KS 的改变的 CpG-甲基化位点，以寻找与 KS 的各种表型或发病机制相关的重要基因。我们进行了全基因组亚硫酸氢盐测序（WGBS）以选择靶 CpG 岛，并在杂交捕获后应用酶促转换技术，以确认来自 65 名参与者、31 名 KS 患者和 34 名未受影响个体的 DNA 样本中 130 个选定的差异甲基化靶区域（DMTR）的 KS 特异性外显子签名。我们在 22 个 DMTR 中鉴定出 26 个候选基因，这些基因可能与 KS 相关。我们的结果表明，可以从少数 WGBS 样本中识别出疾病特异性的甲基化位点，并且杂交捕获后进行酶促甲基化测序可以同时测试这些位点。
尽管 DNA 甲基化可能具有组织特异性，但我们的结果表明，从外周血中提取的 DNA 的甲基化谱分析可能是研究疾病发病机制的有力方法。
