Exploring the role of epigenetic mechanisms in the manifestation of Huntington's disease

探索表观遗传机制在亨廷顿舞蹈病表现中的作用

• 批准号: MR/Y014685/1
• 负责人: Katie Lunnon
• 金额: $ 133.94万
• 依托单位: UNIVERSITY OF EXETER
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2024
• 资助国家: 英国
• 起止时间: 2024 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FY014685%2F1
• 关键词: Exploring; role; epigenetic; mechanisms; manifestation

Huntington's disease (HD) is a neurodegenerative disease caused by an expansion of typically 40 or more repeats of the DNA code "CAG" in the Huntingtin (HTT) gene. The disease is characterised by movement disturbances, cognitive impairments, and psychiatric symptoms and there is currently no disease-modifying treatment. The size of the CAG repeat is closely associated with the age of symptom onset, with individuals with high numbers of repeats developing the disease at a young age. However, there is variation in the age of symptom onset between individuals with the same CAG repeat length. It is known that the expression of genes relies not only on a person's specific DNA code (their genome) but can also be altered by an extra level of information called the "epigenome". Epigenetic processes are chemical tags added to the DNA or histone proteins that turn genes on and off and can be influenced by external factors. We have recently shown robust alterations in two epigenetic marks (DNA methylation (DNAm) and H3K27ac) in Alzheimer's disease (AD). We have also seen DNAm differences in a pilot study of HD brain. We hypothesise that epigenetic mechanisms contribute to the manifestation of HD and plan to use state-of-the art genomic technology and computational approaches to undertake the most comprehensive study of epigenetic mechanisms in HD brain to date. We have the following complimentary work-packages:WP1: (EPI)GENETIC CHARACTERISATION OF HTT USING LONG-READ SEQUENCINGWe will use cutting-edge long-read sequencing technology to measure the length of the CAG repeat and extent of DNAm across that region of the HTT gene. This will allow us to determine exactly where DNAm is seen in the CAG repeat in HD brain samples. We plan to study two brain regions: the striatum and prefrontal cortex, which are affected at different stages of the disease. It is reported that the CAG repeat length can increase in some cells with age, which is termed somatic mosaicism. One advantage of using long-read sequencing is that we can measure both the CAG repeat length and DNAm on the same molecule, which will allow us to explore this phenomenon in our samples.WP2: DECIPHERING THE EPIGENETIC LANDSCAPE IN HD VIA EWASWe will perform the first genome-scale assessment of epigenetic variation in HD brain samples, profiling DNAm, H3K27ac, chromatin accessibility and genetic variation in the striatum and prefrontal cortex. We will investigate whether DNAm, H3K27ac or areas of open chromatin are seen at specific gene regions in HD. As we have generated similar datasets in other neurodegenerative diseases, we can then examine whether there is any overlap in the epigenetic changes we identify in HD to, for example, AD. Using integrative computational approaches, we will explore the relationship between different layers of epigenetic information. By integrating genetic data, we can identify quantitative trait loci (QTLs), where genetic differences alter the epigenetic marks, and then investigate if these QTLs are enriched in genes we know are affected in HD, and other related disorders. WP3: DETERMINING THE CELLULAR SPECIFICITY OF LOCI USING FANSWe will isolate nuclei from different cell types in the prefrontal cortex using fluorescence-activated nuclei sorting (FANS), including inhibitory (GABA) and excitatory (glutamatergic) neurons that are known to be affected in disease, as well as glial cells such as microglia, oligodendrocytes and astrocytes. We will determine which cell types are responsible for the epigenetic changes we observed in the earlier WP in a subset of the cohort with severe pathology (N=20), moderate pathology (N=20) or no pathology (N=20)WP4: CHARACTERISATION OF HTT TRANSCRIPT ISOFORM DIVERSITY IN HDWe will use long-read sequencing to measure expression of the HTT gene, and other genes we have identified. The advantage of this technology is that we can identify completely novel isoforms, which we have previously done in AD.

亨廷顿氏病（HD）是一种神经退行性疾病，原因是Huntingtin（HTT）基因中DNA代码“ CAG”的重复量通常为40或更多。该疾病的特征是运动障碍，认知障碍和精神病症状，目前尚无疾病改良治疗。 CAG重复的大小与症状发作的年龄密切相关，患有大量重复的人在年轻时就会发展该疾病。但是，具有相同CAG重复长度的个体之间的症状发作时代存在差异。众所周知，基因的表达不仅依赖于一个人的特定DNA代码（其基因组），而且还可以通过称为“表观基因组”的额外信息来改变。表观遗传过程是添加到开关和关闭基因的DNA或组蛋白中的化学标签，可能会受到外部因素的影响。我们最近在阿尔茨海默氏病（AD）中显示了两个表观遗传标记（DNA甲基化（DNAM）和H3K27AC）的强大变化。我们还看到了HD大脑的试点研究中的DNAM差异。我们假设表观遗传机制有助于HD的表现，并计划使用最先进的基因组技术和计算方法来进行迄今为止对HD大脑中表观遗传机制的最全面研究。我们有以下免费工作包：WP1：（EPI）使用长阅读Sequencingwe对HTT的遗传表征将使用尖端的长阅读测序技术来衡量CAG重复的长度和DNAM在该区域的DNAM的长度HTT基因。这将使我们能够准确确定在HD脑样品中的CAG重复中看到DNAM的位置。我们计划研究两个大脑区域：纹状体和前额叶皮层，它们在疾病的不同阶段受到影响。据报道，随着年龄的增长，CAG重复长度可以增加，这称为体细胞镶嵌。使用长阅读测序的一个优点是，我们可以在同一分子上测量CAG重复长度和DNAM，这将使我们能够在样品中探索这种现象。WP2：通过Ewaswe在HD中进行表观遗传景观的解密将执行首次基因组规模评估HD脑样品的表观遗传变异，DNAM，H3K27AC，染色质的可及性以及纹状体和前额叶皮层的遗传变异。我们将研究在HD的特定基因区域中是否可以看到DNAM，H3K27AC或开放染色质区域。由于我们已经在其他神经退行性疾病中生成了类似的数据集，因此我们可以检查我们在HD中识别的表观遗传变化是否存在任何重叠，例如AD。使用综合计算方法，我们将探讨表观遗传信息不同层之间的关系。通过整合遗传数据，我们可以识别遗传差异改变表观遗传标记的定量性状基因座（QTL），然后研究这些QTL是否富含我们知道的基因，我们知道在HD和其他相关疾病中受到影响。 WP3：使用粉丝确定基因座的细胞特异性将使用荧光激活的核分类（粉丝）（包括抑制性（GABA）和兴奋性（谷氨酸）神经元）与前额叶皮层中的不同细胞类型分离核，这些核是已知在疾病中受到疾病的影响，以及诸如小胶质细胞，少突胶质细胞和星形胶质细胞等神经胶质细胞。我们将确定哪些细胞类型负责我们在与严重病理（n = 20），中等病理（n = 20）或无病理（n = 20）WP4：中等病理学（n = 20）的一部分中观察到的表观遗传变化。 HTT转录本同工型多样性在HDWE中的表征将使用长阅读测序来测量HTT基因的表达以及我们已经鉴定出的其他基因。这项技术的优点是我们可以识别出完全新颖的同工型，这是我们以前在AD中所做的。