Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
Genetics and Genomic Medicine, Institute of Child Health, University College of London, London, UK.
Sci Rep. 2017 May 26;7(1):2441. doi: 10.1038/s41598-017-02721-0.
Non-syndromic cleft lip and/or palate (NSCLP) is a common congenital malformation with a multifactorial model of inheritance. Although several at-risk alleles have been identified, they do not completely explain the high heritability. We postulate that epigenetic factors as DNA methylation might contribute to this missing heritability. Using a Methylome-wide association study in a Brazilian cohort (67 NSCLP, 59 controls), we found 578 methylation variable positions (MVPs) that were significantly associated with NSCLP. MVPs were enriched in regulatory and active regions of the genome and in pathways already implicated in craniofacial development. In an independent UK cohort (171 NSCLP, 177 controls), we replicated 4 out of 11 tested MVPs. We demonstrated a significant positive correlation between blood and lip tissue DNA methylation, indicating blood as a suitable tissue for NSCLP methylation studies. Next, we quantified CDH1 promoter methylation levels in CDH1 mutation-positive families, including penetrants, non-penetrants or non-carriers for NSCLP. We found methylation levels to be significantly higher in the penetrant individuals. Taken together, our results demonstrated the association of methylation at specific genomic locations as contributing factors to both non-familial and familial NSCLP and altered DNA methylation may be a second hit contributing to penetrance.
非综合征性唇腭裂（NSCLP）是一种常见的先天性畸形，具有多因素遗传模型。尽管已经确定了几个风险等位基因，但它们并不能完全解释高遗传性。我们假设表观遗传因素（如 DNA 甲基化）可能导致了这种缺失的遗传性。我们在巴西队列（67 例 NSCLP，59 例对照）中进行了全基因组甲基化关联研究，发现了 578 个与 NSCLP 显著相关的甲基化可变位置（MVP）。MVP 富集在基因组的调控和活性区域，以及已经涉及颅面发育的途径中。在一个独立的英国队列（171 例 NSCLP，177 例对照）中，我们复制了 11 个测试 MVP 中的 4 个。我们证明了血液和唇组织 DNA 甲基化之间存在显著的正相关，这表明血液是 NSCLP 甲基化研究的合适组织。接下来，我们在包括外显子、非外显子或 NSCLP 非携带者的 CDH1 基因突变阳性家族中定量了 CDH1 启动子甲基化水平。我们发现外显子个体的甲基化水平显著升高。总之，我们的结果表明，特定基因组位置的甲基化与非家族性和家族性 NSCLP 相关，并且 DNA 甲基化的改变可能是导致外显率的第二次打击。
