Impact of DNA double-strand breaks on 3D genome organization and genome stability in Alzheimer’s disease

DNA 双链断裂对阿尔茨海默病 3D 基因组组织和基因组稳定性的影响

基本信息

批准号：
10463836
负责人：
Vishnu Dileep
金额：
$ 13.67万
依托单位：
MASSACHUSETTS INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-08-15 至 2024-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10463836
关键词：
3-Dimensional ATAC-seq Adopted Advisory Committees Aging Alzheimer&apos s Disease Alzheimer&apos s disease brain Alzheimer&apos s disease model Alzheimer&apos s disease risk Autopsy Biological Assay Biology Brain Cells ChIP-seq Chromatin Chromosomal translocation Coculture Techniques Complex DNA DNA Binding DNA Damage DNA Double Strand Break Data Development Disease Disease associated microglia Frequencies Gene Expression Genome Genome Stability Genomic Instability Genomics Goals Hi-C Human Hyperactivity Immediate-Early Genes Induced pluripotent stem cell derived neurons Knockout Mice Label Lead Location Measures Mediating Mentors Mentorship Microglia Mission Modeling Molecular Mosaicism Mus Mutation Nerve Degeneration Neurodegenerative Disorders Neuroglia Neuronal Dysfunction Neurons Nonhomologous DNA End Joining Oligodendroglia Orthologous Gene Partner in relationship Pathogenesis Pathologic Pathway interactions Pattern Pharmacology Phase Play Public Health Publishing Recurrence Reporting Role Tauopathies Technology Testing Therapeutic Intervention Training Work aging brain cell type chromosome conformation capture cohesin computational pipelines experience familial Alzheimer disease improved in situ sequencing induced pluripotent stem cell induced pluripotent stem cell technology mouse model nervous system disorder novel novel therapeutics presenilin-1 prevent promoter response single cell analysis single-cell RNA sequencing therapeutic evaluation tool transcription factor transcriptome

项目摘要

PROJECT SUMMARY/ABSTRACT The accumulation of DNA Double-Strand Breaks (DSBs) in neurons is an early hallmark of Alzheimer’s disease (AD). Increased DSBs are also associated with aging, which is the largest risk factor for AD. AD is also a complex disease involving all major brain glial cell types. Thus, there is a critical need to understand the molecular mechanisms of DSB induced changes in both neurons and glia. The structural stability of the genome is paramount in maintaining a functional genome, and recently, the 3D organization of the genome has emerged as a major regulator of genome function. My overall hypothesis is that 3D genome reorganization and structural genome instability mediated by DSBs are principle drivers of AD pathogenesis and brain aging. My objective is to determine how and to what extent DSBs within the neurons impact genome organization and the glial response, with the goal of identifying molecular pathways that can be targeted as novel therapies for preventing or halting the progression of neurodegeneration. I will use mouse models that recapitulate the pre-symptomatic accumulation of DSBs in neurons and human iPSC models to determine the degree of the 3D genome disruption caused due to DSBs and the underlying molecular mechanisms. I will also identify the consequences of neuronal DSBs on the structural stability of the genome by measuring the frequency of DSB mediated chromosomal translocations in human AD neurons. Interestingly, normal neuronal activity causes DSBs at immediate early gene promoters. Also, neuronal hyperactivity has been reported in AD. I will test if IEGs are locations of frequent chromosomal translocations after neuronal hyperactivity induced in neuronal culture. Previous studies have shown that microglia transitions to a reactive state in response to neurodegeneration. To understand the role of the 3D genome organization in this microglia transition, I will use single cell Hi-C to measure the unique chromatin interactions that mediate the reactive microglia state. Subsequently, transcription factor predictions using integrative analysis of single cell Hi-C will be tested in iPSC derived microglia-neuron co-cultures for their potential to modulate the reactive microglia response. This approach will be extended to study oligodendrocyte response in the independent phase. I will work with my mentor Dr. Li-Huei Tsai, my mentorship committee, Dr. Bruce Yankner and Dr. Manolis Kellis, my technical support and advisory committee, Dr. Frederick Alt and Dr. Peter Fraser to carry out my proposed training plan. I will gain experience in iPSC technology and differentiation from the Tsai lab to modulate the disease associated microglia response to neuronal DSBs and work with Dr. Manolis Kellis to implement the computational pipelines for the transcription factor predictions. To bridge the gap in my training in the biology of AD and brain aging, I will audit relevant courses and receive additional mentoring from Dr. Bruce Yankner.

项目概要/摘要神经元中 DNA 双链断裂 (DSB) 的积累是阿尔茨海默病的早期标志 DSB 增加也与衰老有关，这是 AD 的最大危险因素，也是一个复杂的因素。涉及所有主要脑神经胶质细胞类型的疾病因此，迫切需要了解其分子机制。 DSB 诱导神经元和神经胶质细胞变化的机制是基因组的结构稳定性。对于维持功能基因组至关重要，最近，基因组的 3D 组织已经出现我的总体假设是 3D 基因组重组和结构。 DSB 介导的基因组不稳定性是 AD 发病机制和大脑衰老的主要驱动因素。确定神经元内的 DSB 如何以及在何种程度上影响基因组组织和神经胶质细胞反应，目标是确定可作为预防新疗法的分子途径或阻止神经退行性变的进展，我将使用重现症状前的小鼠模型。 DSB 在神经元和人类 iPSC 模型中的积累，以确定 3D 基因组破坏的程度由于 DSB 和潜在的分子机制引起的，我还将确定神经的后果。通过测量 DSB 介导的染色体频率来观察 DSB 对基因组结构稳定性的影响人类 AD 神经元中的易位表明，正常的神经元活动会在早期引起 DSB。此外，AD 中也有神经元过度活跃的报道，我将测试 IEG 是否是频繁出现的位置。神经过度活跃诱导神经培养物活动后的染色体易位。先前的研究表明，小胶质细胞会转变为反应状态以响应为了了解 3D 基因组组织在小胶质细胞转变中的作用，我将使用单细胞 Hi-C 来测量介导反应性小胶质细胞状态的独特染色质相互作用。随后，将在 iPSC 中测试使用单细胞 Hi-C 综合分析的转录因子预测衍生的小胶质细胞-神经元共培养物具有调节反应性小胶质细胞反应的潜力。该方法将扩展到研究独立阶段少突胶质细胞的反应。我将与我的导师 Li-Huei Tsai 博士、我的导师委员会 Bruce Yankner 博士和 Manolis 博士一起工作凯利斯 (Kellis)、我的技术支持和咨询委员会、弗雷德里克·阿尔特 (Frederick Alt) 博士和彼得·弗雷泽 (Peter Fraser) 博士来执行我的我将从 Tsai 实验室获得 iPSC 技术和分化方面的经验来进行调整。与疾病相关的小胶质细胞对神经元 DSB 的反应，并与 Manolis Kellis 博士合作实施转录因子预测的计算管道弥补了我在生物学训练中的差距。 AD 和大脑老化，我将旁听相关课程并接受 Bruce Yankner 博士的额外指导。