Do oxidative breaks accumulate at gene regulatory regions in disease?

疾病中的基因调控区域是否会积累氧化断裂？

• 批准号: MR/Y000021/1
• 负责人: Sherif El-Khamisy
• 金额: $ 70.94万
• 依托单位: University of Sheffield
• 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%2FY000021%2F1
• 关键词: Do; oxidative; breaks; accumulate; gene

The recent revolution in genomics aspires to provide better understanding of how changes in the DNA sequence cause disease, which will improve health outcomes by providing better diagnostics and therapeutics. This could be achieved by developing smart sequencing panels for early diagnosis and exploiting vulnerabilities in DNA repair to treat cancer or correcting single gene disorders using gene editing and replacement in neurological disease. Although many patterns of mutation (signatures) arise due to defective DNA repair, some remain of unknown aetiology, and how they lead to disease phenotype is often unknown. Therefore, there is a need to define biological mechanisms generating such mutations and determine their link to human disease. So far, the role of many mutation signatures has only been studied in protein-coding parts of the genome. However, recently, we have found that oxidative DNA breaks and abasic sites arise in the regulatory parts of mammalian genomes and described a mechanism for their repair (Ray et al., Nature 609 :1038-1047, 2022). Although increased oxidative stress is associated with several neurological disorders, the mechanistic pathway from this to disease is currently unclear. We propose that oxidative DNA breaks may accumulate at gene regulatory regions and that these regions may exhibit increased mutational burden reminiscent of defective oxidative break repair, eventually leading to their malfunction and disease phenotypes. In this project, we will investigate oxidative DNA breaks at regulatory genomic regions in two neurological diseases caused by defects in the DNA repair proteins, tyrosyl DNA phosphodiesterase I (TDP1) and ataxia telangiectasis mutated (ATM). We will do so by: 1. Determining the profile of oxidative DNA breaks in patient derived neurons using genomic mapping methods that we recently described in Ray et al., 2022. 2. Establishing the source of endogenous oxidative breaks at gene regulatory regions in patient derived neurons, by genetic and chemical manipulations 3. Exploring the impact of unrepaired oxidative breaks on the early stages of the transcription cycle, using methods that we recently described in Ray et al., 2022.4. Determining whether the mutational burden is increased at gene regulatory regions in patient derived cells Revealing how oxidative breaks impact gene regulatory regions and transcriptional responses will increase our understanding of the aetiology of these two neurological diseases and pave the way of similar approaches in other neurological disease that feature increased oxidative stress but not directly linked to mutations of DNA repair proteins, such as Alzheimer's disease and dementia.

最近的基因组学革命希望更好地了解DNA序列的变化如何导致疾病，这将通过提供更好的诊断和治疗来改善健康结果。这可以通过开发用于早期诊断的智能测序面板和利用DNA修复中的漏洞来治疗癌症或使用基因编辑和神经系统疾病中的替代来纠正单基因疾病来实现。 虽然许多突变模式（签名）是由于DNA修复缺陷引起的，但有些仍然是未知的病因，并且它们如何导致疾病表型通常是未知的。因此，需要定义产生此类突变的生物学机制并确定它们与人类疾病的联系。到目前为止，许多突变标签的作用仅在基因组的蛋白质编码部分中进行了研究。然而，最近，我们发现氧化性DNA断裂和脱碱基位点出现在哺乳动物基因组的调控部分中，并描述了它们的修复机制（Ray et al.，Nature 609：1038-1047，2022）。虽然增加的氧化应激与几种神经系统疾病有关，但从这到疾病的机制途径目前尚不清楚。我们提出，氧化DNA断裂可能会积累在基因调控区，这些地区可能会表现出增加的突变负担，让人想起有缺陷的氧化断裂修复，最终导致其功能障碍和疾病表型。在这个项目中，我们将调查氧化DNA断裂在两个神经系统疾病的DNA修复蛋白，酪氨酰DNA磷酸二酯酶I（TDP 1）和共济失调毛细血管扩张症突变（ATM）的缺陷引起的基因组调控区域。我们将这样做：1。使用我们最近在Ray等人，2022. 2.通过遗传和化学操作，在患者源性神经元的基因调控区建立内源性氧化断裂的来源3。探索未修复的氧化断裂对转录周期早期阶段的影响，使用我们最近在Ray等人中描述的方法，2022.4.确定患者来源的细胞中基因调控区的突变负荷是否增加揭示氧化断裂如何影响基因调控区和转录反应将增加我们对这两种神经系统疾病病因的理解，并为其他神经系统疾病的类似方法铺平道路，这些疾病的特征是氧化应激增加，但与DNA修复蛋白的突变没有直接联系，如阿尔茨海默病和痴呆症。