唐氏综合征新生儿主要先天性心脏病的表观基因组特征

Epigenomic signature of major congenital heart defects in newborns with Down syndrome.

作者信息

Mouat Julia S, Li Shaobo, Myint Swe Swe, Laufer Benjamin I, Lupo Philip J, Schraw Jeremy M, Woodhouse John P, de Smith Adam J, LaSalle Janine M

机构信息

Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA.

Perinatal Origins of Disparities Center, University of California, Davis, CA USA.

出版信息

medRxiv. 2023 May 5:2023.05.02.23289417. doi: 10.1101/2023.05.02.23289417.

BACKGROUND

Congenital heart defects affect approximately half of individuals with Down syndrome but the molecular reasons for incomplete penetrance are unknown. Previous studies have largely focused on identifying genetic risk factors associated with CHDs in individuals with DS, but comprehensive studies of the contribution of epigenetic marks are lacking. We aimed to identify and characterize DNA methylation differences from newborn dried blood spots of DS individuals with major CHDs compared to DS individuals without CHDs.

METHODS

We used the Illumina EPIC array and whole-genome bisulfite sequencing to quantitate DNA methylation for 86 NDBS samples from the California Biobank Program: 1) 45 DS-CHD (27 female, 18 male) and 2) 41 DS non-CHD (27 female, 14 male). We analyzed global CpG methylation and identified differentially methylated regions in DS-CHD vs DS non-CHD comparisons (both sex-combined and sex-stratified) corrected for sex, age of blood collection, and cell type proportions. CHD DMRs were analyzed for enrichment in CpG and genic contexts, chromatin states, and histone modifications by genomic coordinates and for gene ontology enrichment by gene mapping. DMRs were also tested in a replication dataset and compared to methylation levels in DS vs typical development WGBS NDBS samples.

RESULTS

We found global CpG hypomethylation in DS-CHD males compared to DS non-CHD males, which was attributable to elevated levels of nucleated red blood cells and not seen in females. At a regional level, we identified 58, 341, and 3,938 CHD-associated DMRs in the Sex Combined, Females Only, and Males Only groups, respectively, and used machine learning algorithms to select 19 Males Only loci that could distinguish CHD from non-CHD. DMRs in all comparisons were enriched for gene exons, CpG islands, and bivalent chromatin and mapped to genes enriched for terms related to cardiac and immune functions. Lastly, a greater percentage of CHD-associated DMRs than background regions were differentially methylated in DS vs TD samples.

CONCLUSIONS

A sex-specific signature of DNA methylation was detected in NDBS of DS-CHD compared to DS non-CHD individuals. This supports the hypothesis that epigenetics can reflect the variability of phenotypes in DS, particularly CHDs.

背景

先天性心脏病影响约一半的唐氏综合征患者，但不完全外显的分子原因尚不清楚。以往的研究主要集中在识别唐氏综合征患者中与先天性心脏病相关的遗传风险因素，但缺乏对表观遗传标记贡献的全面研究。我们旨在识别和表征患有主要先天性心脏病的唐氏综合征个体与未患先天性心脏病的唐氏综合征个体的新生儿干血斑中的DNA甲基化差异。

方法

我们使用Illumina EPIC阵列和全基因组亚硫酸氢盐测序对来自加利福尼亚生物样本库计划的86份新生儿干血斑样本进行DNA甲基化定量：1）45例唐氏综合征合并先天性心脏病（27例女性，18例男性）和2）41例唐氏综合征无先天性心脏病（27例女性，14例男性）。我们分析了整体CpG甲基化，并在针对性别、采血年龄和细胞类型比例进行校正的唐氏综合征合并先天性心脏病与唐氏综合征无先天性心脏病比较（包括性别合并和性别分层）中鉴定了差异甲基化区域。通过基因组坐标分析先天性心脏病相关差异甲基化区域在CpG和基因背景、染色质状态和组蛋白修饰方面的富集情况，并通过基因映射分析基因本体富集情况。差异甲基化区域也在一个复制数据集中进行了测试，并与唐氏综合征与典型发育的全基因组亚硫酸氢盐测序新生儿干血斑样本中的甲基化水平进行了比较。

结果

我们发现与唐氏综合征无先天性心脏病男性相比，唐氏综合征合并先天性心脏病男性存在整体CpG低甲基化，这归因于有核红细胞水平升高，在女性中未观察到。在区域水平上，我们分别在性别合并组、仅女性组和仅男性组中鉴定出58个、341个和3938个与先天性心脏病相关的差异甲基化区域，并使用机器学习算法选择了19个仅男性位点，这些位点可以区分先天性心脏病和非先天性心脏病。所有比较中的差异甲基化区域在基因外显子、CpG岛和二价染色质中富集，并映射到与心脏和免疫功能相关术语富集的基因上。最后，与背景区域相比，更多比例的与先天性心脏病相关的差异甲基化区域在唐氏综合征与典型发育样本中存在差异甲基化。