Whole genome bisulfite sequencing of Down syndrome brain reveals regional DNA hypermethylation and novel disorder insights

Down Syndrome (DS) is the most common genetic cause of intellectual disability, in which an extra copy of human chromosome 21 (HSA21) affects regional DNA methylation profiles across the genome. Although DNA methylation has been previously examined at select regulatory regions across the genome in a variety of DS tissues and cells, differentially methylated regions (DMRs) have yet to be examined in an unbiased sequencing-based approach. Here, we present the first analysis of DMRs from whole genome bisulfite sequencing (WGBS) data of human DS and matched control brain, specifically frontal cortex. While no global differences in DNA methylation were observed, we identified 3,152 DS-DMRs across the entire genome, the majority of which were hypermethylated in DS. DS-DMRs were significantly enriched at CpG islands and de-enriched at specific gene body and regulatory regions. Functionally, the hypermethylated DS-DMRs were enriched for one-carbon metabolism, membrane transport, and glutamatergic synaptic signalling, while the hypomethylated DMRs were enriched for proline isomerization, glial immune response, and apoptosis. Furthermore, in a cross-tissue comparison to previous studies of DNA methylation from diverse DS tissues and reference epigenomes, hypermethylated DS-DMRs showed a strong cross-tissue concordance, while a more tissue-specific pattern was observed for the hypomethylated DS-DMRs. Overall, this approach highlights that low-coverage WGBS of clinical samples can identify epigenetic alterations to known biological pathways, which are potentially relevant to therapeutic treatments and include metabolic pathways. These results also provide new insights into the genome-wide effects of genetic alterations on DNA methylation profiles indicative of altered neurodevelopment and brain function.

唐氏综合征（Down Syndrome, DS）是最常见的遗传性智力障碍病因，患者体内存在人类21号染色体（human chromosome 21, HSA21）的额外拷贝，该染色体异常会影响全基因组范围内的区域DNA甲基化谱。此前虽已在多种DS组织及细胞的基因组特定调控区域开展过DNA甲基化相关研究，但尚未有基于无偏测序方法的差异甲基化区域（differentially methylated regions, DMRs）相关分析。
本研究首次针对人类DS及匹配对照的全基因组亚硫酸氢盐测序（whole genome bisulfite sequencing, WGBS）数据中的DMRs展开分析，研究样本取自前额叶皮层脑组织。尽管未观察到全基因组水平的DNA甲基化整体差异，我们在全基因组范围内鉴定出3152个DS相关DMRs（DS-DMRs），其中多数在DS样本中呈高甲基化状态。
DS-DMRs在CpG岛处显著富集，而在特定基因本体区域及调控区域则呈现去富集特征。功能富集分析显示，高甲基化DS-DMRs显著富集于一碳代谢、膜转运及谷氨酸能突触信号通路等生物学过程；低甲基化DS-DMRs则富集于脯氨酸异构化、胶质细胞免疫应答及细胞凋亡等通路。
此外，通过与此前针对多种DS组织及参考表观基因组的DNA甲基化研究开展跨组织比较，我们发现高甲基化DS-DMRs在跨组织层面表现出高度一致性，而低甲基化DS-DMRs则呈现更强的组织特异性模式。
总体而言，本研究表明，针对临床样本的低覆盖度WGBS可鉴定出与已知生物学通路相关的表观遗传改变，这类改变或与临床治疗相关，且涵盖代谢通路。本研究结果还为解析遗传改变通过调控DNA甲基化谱式进而影响神经发育与脑功能的全基因组效应提供了全新的认知。