Tissue Specific Methylation and Expression Patterns of ADCA-DN Patients. Tissue Specific Methylation and Expression Patterns of ADCA-DN Patients

Autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCA-DN) is a late onset disorder, due to mutations in DNA methyltransferase type 1 (DNMT1). Yet our understanding of how these mutations in DNMT1 lead to the clinical phenotypes of ADCA-DN is still unclear. To address this, we used fibroblasts, induced pluripotent stem cells (iPSCs) and induced neurons (iNs) generated from patients with ADCA-DN and controls, to determine the underlining epigenomic changes. Here we show that the differential expression pattern and differential methylation spectrum between patients and controls were tissue-specific. Furthermore, methylation and gene expression changes were negatively correlated in iPSCs and iNs. In addition, we identified a group of genes associated with clinical phenotypes of ADCA-DN, including PDGFB and PRDM8 for cerebellar ataxia, psychosis and dementia, and NR2F1 for deafness and optic atrophy. We further showed that ZFP57, which is required to maintain gene imprinting through DNA methylation during early development, was hypomethylated in promoters and exhibited upregulated expression in patients with ADCA-DN in both iPSC and iNs. Our results provide insight into the molecular changes associated with ADCA-DN, with potential implications for genes associated with related phenotypes. Overall design: Investigated tissue specific DNA methylation and gene expression patterns in induced neurons derived from induced pluripotent stem cells (iPSCs) from patients with ADCA-DN.

常染色体显性遗传性小脑共济失调、耳聋与发作性睡病（Autosomal dominant cerebellar ataxia, deafness, and narcolepsy, ADCA-DN）是一种迟发性疾病，由1型DNA甲基转移酶（DNA methyltransferase type 1, DNMT1）突变引发。目前学界对这类DNMT1突变如何导致ADCA-DN的临床表型仍不甚明确。为阐明该科学问题，本研究利用ADCA-DN患者与健康对照来源的成纤维细胞、诱导多能干细胞（induced pluripotent stem cells, iPSCs）以及诱导神经元（induced neurons, iNs），探究其潜在的表观基因组改变。研究结果显示，患者与对照组之间的差异表达谱与差异甲基化谱均具有组织特异性；进一步分析发现，在iPSCs与iNs中，甲基化水平与基因表达变化呈负相关。此外，本研究鉴定出一组与ADCA-DN临床表型相关的基因：其中PDGFB与PRDM8与小脑共济失调、精神病及痴呆相关，NR2F1与耳聋和视神经萎缩相关。本研究还发现，在早期发育过程中通过DNA甲基化维持基因印记所必需的ZFP57，在ADCA-DN患者的iPSCs与iNs中，其启动子区域呈低甲基化状态，且基因表达上调。本研究结果为解析ADCA-DN相关的分子改变提供了新的视角，也为关联相关表型的基因研究提供了潜在方向。整体实验设计：对ADCA-DN患者来源诱导多能干细胞分化得到的诱导神经元，开展组织特异性DNA甲基化与基因表达模式分析。