Single-cell analysis of DNA damage, somatic mutation, and gene expression in human Alzheimer’s disease brain

对人类阿尔茨海默病大脑中 DNA 损伤、体细胞突变和基因表达的单细胞分析

• 批准号: 10901006
• 负责人: Michael Anthony Lodato
• 金额: $ 83.58万
• 依托单位: UNIV OF MASSACHUSETTS MED SCH WORCESTER
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10901006
• 关键词: 1 year old; Affect; Age; Aging; Alzheimer' s Disease; Alzheimer' s disease brain; Alzheimer' s disease pathology; Alzheimer' s disease patient; Alzheimer' s disease risk; Area; Autopsy; Base Pairing; Biochemical; Biology of Aging; Birth; Brain; Cell Nucleus; Cell physiology; DNA Damage; DNA Repair; DNA Repair Gene; DNA Repair Pathway; DNA analysis; DNA lesion; Data; Disease; Disease Progression; Elderly; Enhancers; Event; Exhibits; Exposure to; Freezing; Functional disorder; Gene Expression; Generations; Genetic Enhancer Element; Genetic Transcription; Genome; Genomics; Goals; Histologic; Human; Immunofluorescence Immunologic; Individual; Literature; Malignant Neoplasms; Methods; Microglia; Mutagens; Mutation; Nerve Degeneration; Neurodegenerative Disorders; Neurofibrillary Tangles; Neuronal Dysfunction; Neurons; Onset of illness; Pathogenesis; Pathogenicity; Pathway interactions; Pattern; Post-Translational Protein Processing; Process; Proteins; Proteomics; Protocols documentation; Publishing; Risk Factors; Sampling; Scientist; Senile Plaques; Shapes; Single Nucleotide Polymorphism; Somatic Mutation; Source; Stains; Stereotyping; Testing; Variant; Work; age related; cell type; disorder risk; excitatory neuron; healthy aging; human old age (65+); improved; innovation; insertion/deletion mutation; insight; mind control; misfolded protein; neurodegenerative phenotype; neuron loss; neuronal patterning; neuropathology; new technology; normal aging; oxidative damage; postmitotic; programs; protein aggregation; protein misfolding; single cell analysis; single nucleus RNA-sequencing; tau Proteins; transcriptome; transcriptomics; translational potential; tumor

Project Summary Alzheimer’s disease (AD) displays an age-related disease onset, but the mechanisms by which age influences disease risk are unknown. DNA damage is a hallmark of normal aging and has been implicated as a possible pathogenic mechanism in AD. We recently innovated new methods to study the genome of single neurons from the postmortem human brain. Using these novel technologies, we showed that normal neurons contain at least dozens of somatic single nucleotide variants (SNVs) per genome at birth. Somatic SNVs increase linearly in postmitotic neurons after birth, reaching levels in the thousands in old age. Somatic SNVs can be analyzed by patterns of base-pair substitution, analogous to cancer mutations, where distinct mutational “signatures” mark tumors exposed to specific mutagens or those with deficiencies in specific DNA damage repair pathways. This analysis of our data revealed at least two neuronal mutational signatures arising in neurons from distinct sources: one related to aging generally, another related to oxidative damage in aging but especially in neurodegeneration. Analysis of the genomic distribution of neuronal somatic SNVs revealed an enrichment in transcribed regions and in active enhancer elements, suggesting that somatic mutations directly impact gene expression networks. These preliminary data suggest an approach to exploring mechanisms of neuronal dysfunction in AD that may be downstream of known risk factors such as protein misfolding. In our recently published work, we showed that somatic SNVs are increased in excitatory neurons of late-stage AD patients. These findings prompted several additional questions. First, at what stage of AD progression does increased somatic mutation begin? To answer this question. we will use a new and improved scWGS protocol to perform a comprehensive analysis of patterns of somatic mutation over the course of AD, including SNV and other types of variants, such as short indels and structural variants. Second, does somatic mutation result in dysregulation in gene expression? We will apply single-nucleus RNA-sequencing to AD and control brains to answer this question. Finally, how does the activity of DNA repair proteins impact the generation of somatic mutations? We will apply a quantitative approach to immunofluorescence staining for various DNA repair proteins and other marks of DNA damage on brian donors with known levels of somatic mutation to identify the root causes of mutation in the human brain. Thus, this proposal aims to understand when somatic mutations occur, what the result of those mutations are, and what caused them in the first place.

项目总结