SINGLE-CELL ANALYSIS OF SOMATIC MUTATION IN AGING ANO NEUROOEGENERATIVE DISEASE IN THE HUMAN BRAIN

人脑衰老和神经生成疾病中体细胞突变的单细胞分析

• 批准号: 10237914
• 负责人: Michael Anthony Lodato
• 金额: $ 24.58万
• 依托单位: UNIV OF MASSACHUSETTS MED SCH WORCESTER
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-07-01 至 2023-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10237914
• 关键词: Adult; Affect; Age; Aging; Alzheimer' s Disease; Alzheimer' s disease pathology; Alzheimer' s disease patient; Antibiotics; Antioxidants; Authorship; Award; Base Pairing; Bioinformatics; Boston; Brain; Cardiovascular Diseases; Cells; Cerebral cortex; Characteristics; Cockayne Syndrome; Communities; DNA; DNA Damage; DNA Markers; DNA Sequence Alteration; DNA sequencing; Data; Development; Diabetes Mellitus; Disease; Doctor of Medicine; Doctor of Philosophy; Educational workshop; Elderly; Environment; Epigenetic Process; Equipment; Faculty; Fellowship; Genes; Genetic; Genetic Transcription; Genome; Genomics; Genotoxic Stress; Goals; Health; Human; Human Genome Project; Human body; Incidence; Individual; Inherited; Institutes; Institution; Laboratories; Lesion; Life; Malignant Neoplasms; Manuscripts; Massachusetts; Mediating; Mentors; Mitotic; Molecular Biology; Mutation; Mutation Analysis; Nerve Degeneration; Nervous System Physiology; Nervous system structure; Neurobiology; Neurodegenerative Disorders; Neurons; Nucleotides; Oxidative Stress; Paper; Pathogenicity; Pathologic Mutagenesis; Pathway interactions; Patients; Pattern; Pediatric Hospitals; Peer Review; Persons; Phase; Phenotype; Positioning Attribute; Postdoctoral Fellow; Production; Progeria; Proteins; Publications; Publishing; Reactive Oxygen Species; Reagent; Research; Research Personnel; Research Training; Risk Factors; Role; Sampling; Scanning Electron Microscopy; Science; Secure; Single Nucleotide Polymorphism; Somatic Mutation; Supervision; Technology; Testing; Tissue Culture Techniques; Tissues; Universities; Variant; Walking; Work; Xeroderma Pigmentosum; age group; age related; aging brain; base; body system; career; career development; cognitive function; experience; experimental study; genome integrity; genome sequencing; human disease; interest; loss of function; loss of function mutation; medical schools; meetings; novel; oxidative DNA damage; post-doctoral training; repaired; response; single cell analysis; single cell sequencing; skills; stem; success; supportive environment; tenure track; transdifferentiation; undergraduate student; virtual; whole genome

Project Summary/Abstract Candidate. I have a profound interest in understanding the genetic and epigenetic mechanisms that control cell state, and have built upon that interest during my research career. As an undergraduate researcher in the laboratory of Dr. Joanne Wiley at Hofstra University, I studied bacterial sporulation and antibiotic production using genetics and scanning electron microscopy, resulting in authorship on a peer-reviewed manuscript. As a Ph.D. candidate in the laboratory of Dr. Rudolf Jaenisch at the Massachusetts Institute of Technology, I worked on several of projects which resulted in authorship of peer-reviewed manuscripts, related to epigenetics, factor- mediated reprogramming, and transdifferentiation. In my main thesis work, I used genomics, genetics, molecular biology, and tissue culture techniques to study cell fate transitions in the development of the mammalian nervous system, resulting in a first-author publication (Lodato et al., PLoS Genetics, 2013, PMID 23437007). In the first part of my postdoctoral fellowship, in the lab of Dr. Christopher Walsh of Boston Children’s Hospital and Harvard Medical School, I built upon all these previous experiences, in particular in using genomics to understand principles of neurobiology, to study somatic mutations in the normal human brain using cutting-edge single-cell whole genome sequencing (WGS) technologies, resulting in a first-author manuscript (Lodato et al., Science, 2015, PMID 26430121). This paper was the first published work to compare the whole-genome rates and characteristics of somatic mutations across normal human individuals, and the expertise I gained developing that technology has prepared me thoroughly to now compare the rates and characteristics of somatic mutations between age groups and in human age-related diseases. The K99/R00 Pathway to Independence Award is the perfect mechanism to help propel me to my scientific and career goals. Under this award, I will 1) Execute a research plan to uncover the role of somatic mutation in aging and in age-related diseases 2) Gain scientific skills and refine my understanding of key concepts in the fields of aging and bioinformatics 3) Undertake career development activities under the supervision of my mentor, co-mentor, and other faculty advisors committed to my successful transition from postdoctoral fellow to independent investigator. Environment. The proposed Research and Training plans will take place in the laboratory of Christopher A. Walsh, M.D., Ph.D., within Boston Children’s Hospital (BCH) and Harvard Medical School (HMS). These institutions comprise a strong, well-established research community, and are committed to the success of the aims and goals proposed in this application. Dr. Walsh has a strong track record of training postdoctoral fellows, many of his former trainees now holding tenured or tenure-track faculty positions at academic institutions. This success stems from the rigorous and supportive environment in the lab, including frequent lab meetings and one-on-one interactions with Dr. Walsh. Scientifically, the lab is supplied with virtually all reagents and equipment needed for the proposed research, and as a part of the greater BCH and HMS community any additional equipment are available within walking distance. The BCH/HMS community is also an asset to the career development aspects of this proposal, providing easy access to potential collaborators and frequent seminars hosting internal and external speakers. As part of this community, and I have secured a co-mentor (Dr. Peter Park, HMS), and two additional faculty advisors (Drs. Bruce Yanker, HMS, and Emanuela Gussoni, BCH/HMS), all committed to my success. Finally, the BCH/HMS environment provides myriad formal career development seminars and workshops, which I will take part in to aid my transition to independence. Research. Advanced age is a major risk factor for human diseases in all organ systems, yet how the phenomenon of aging affects such a wide spectrum of tissues is unknown. All tissues rely on the integrity of the genome to function properly, and one attractive and long-standing hypothesis is that the gradual accumulation of DNA damage might be causal in aging. Proof of this notion has remained elusive in the brain, since standard DNA-sequencing experiments are ill-suited to detect somatic mutations which might mark only a few cells, or even a single cell, in a sample comprised of millions. I have pioneered the use of single-cell, whole-genome sequencing technology to compare rates, characteristics, and consequences of somatic mutations across human brains, and will use this technology as a part of this award to achieve three Aims: 1) Determine whether aging is associated with an accumulation of mutations in the human brain and define patterns of somatic mutation during aging, 2) Single-cell sequencing in progeroid diseases associated with DNA-damage response, and 3) Examination of the somatic mutation rate in Alzheimer’s disease. Thus, this proposal represents a comprehensive body of work that will elucidate the role of somatic mutation in during aging, in accelerated aging, and in age-associated disease in the human brain.

项目摘要/摘要 候选人。我对理解控制的遗传和表观遗传机制有深远的兴趣 细胞状态，并在我的研究生涯中建立了这种兴趣。作为一名本科研究员 霍夫斯特拉大学Joanne Wiley博士的实验室，我研究了细菌孢子型和抗生素生产 使用遗传学和扫描电子显微镜，从而在同行评审的手稿上获得作者身份。作为 博士我在马萨诸塞州理工学院的鲁道夫·贾尼斯（Rudolf Jaenisch）博士实验室的候选人，我工作过 在几个项目中，这些项目导致了同行评审的手稿的作者，与表观遗传学，因子 - 介导的重编程和转分化。在我的主要论文工作中，我使用了基因组学，遗传学， 分子生物学和组织培养技术，用于研究细胞脂肪转变的发展 哺乳动物神经系统，导致第一任作者出版（Lodato等，PLOS Genetics，2013年，PMID 23437007）。在我博士后奖学金的第一部分，在波士顿的克里斯托弗·沃尔什博士的实验室 儿童医院和哈佛医学院，我基于所有以前的经历，尤其是在 使用基因组学了解神经生物学的原理，研究正常人的体细胞突变 使用尖端单细胞全基因组测序（WGS）技术的大脑，导致了第一任作者 手稿（Lodato等，Science，2015，PMID 26430121）。本文是第一个发表的作品 比较正常人中体细胞突变的整个基因组率和特征， 我获得的专业知识已经为我做好了彻底的准备，以比较利率 年龄组和与人类年龄相关疾病之间的体细胞突变的特征。 K99/R00独立奖奖是帮助我推荐我的完美机制 科学和职业目标。根据该奖项，我将1）执行研究计划以揭示躯体的作用 衰老和与年龄有关的疾病的突变2）获得科学技能并完善我对关键的理解 衰老和生物信息学领域的概念3）从事职业发展活动 对我的心理，联合学和其他教师顾问的监督，致力于我成功过渡 博士后研究员与独立调查员。 环境。拟议的研究和培训计划将在ChristopherA的实验室进行。 沃尔什（Walsh，M.D.），博士学位，波士顿儿童医院（BCH）和哈佛医学院（HMS）内。这些 机构构成了一个强大，建立了良好的研究社区，并致力于成功 本应用程序中提出的目标和目标。沃尔什博士在训练博士后有很强的记录 研究员，他的许多以前的培训现在在学术上担任任期或任期教师职位 机构。这种成功源于实验室中严格和支持的环境，包括经常实验室 会议和与沃尔什博士一对一的互动。从科学上讲，实验室几乎全部提供 拟议的研究所需的试剂和设备，以及大型BCH和HMS的一部分 社区任何其他设备都可以在步行距离内提供。 BCH/HMS社区也是 该提案的职业发展方面的资产，可轻松访问潜在的合作者 并经常托管内部和外部扬声器。作为这个社区的一部分，我获得了 联盟（HMS Peter Park博士）和另外两名教师顾问（Bruce Yanker博士，HMS和Emanuela Gussoni，BCH/HMS），都致力于我的成功。最后，BCH/HMS环境提供了无数的正式 职业发展的半身和讲习班，我将参加，以帮助我过渡到独立。 研究。高龄是所有器官系统中人类疾病的主要危险因素，但是 衰老的现象会影响如此广泛的组织。所有组织都依赖于 正常运作的基因组以及一个有吸引力的长期假设是等级 DNA损伤的积累可能是衰老的原因。这个概念的证据在大脑中仍然难以捉摸， 由于标准DNA测序实验不适合检测可能仅标记的体细胞突变 在数百万的样品中，几个单元，甚至一个单元。我已经开创了单细胞的使用， 全基因组测序技术以比较体细胞的速率，特征和后果 人类大脑的突变，并将将该技术用作该奖项的一部分，以实现三个目标：1） 确定衰老是否与人脑突变的积累有关并定义 衰老过程中的体细胞突变模式，2）与相关的后代疾病中的单细胞测序 DNA破坏反应和3）检查阿尔茨海默氏病的体细胞突变率。那，这个 提案代表了一项全面的工作，将阐明在期间体细胞突变的作用 衰老，加速衰老和人脑与年龄相关的疾病。

项目成果

Persistent DNA damage associated with ATM kinase deficiency promotes microglial dysfunction.

• DOI: 10.1093/nar/gkac104
• 发表时间: 2022-03-21
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Bourseguin J;Cheng W;Talbot E;Hardy L;Lai J;Jeffries AM;Lodato MA;Lee EA;Khoronenkova SV
• 通讯作者: Khoronenkova SV

Single-cell transcriptomic and genomic changes in the aging human brain.

衰老人脑中的单细胞转录组和基因组变化。

• DOI: 10.1101/2023.11.07.566050
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Jeffries,AilsaM;Yu,Tianxiong;Ziegenfuss,JenniferS;Tolles,AllieK;Kim,Yerin;Weng,Zhiping;Lodato,MichaelA
• 通讯作者: Lodato,MichaelA