Charting somatic evolution via single-cell multiomics

项目总结 这份提案为Caleb Lareau博士概述了一个为期五年的职业发展计划，为他做好准备 在人类基因组学领域从事独立研究，研究复杂的细胞过程 疾病。候选人将在斯坦福大学进行博士后培训，该大学提供 出色的环境来完成建议的研究和发展大规模计算的技能 分析、基因组学技术发展和免疫学。拉罗博士的导师和顾问，包括 萨特帕西博士、昆达杰博士、格林利夫博士、霍伊特博士、柯蒂斯博士和安德森博士拥有与 建议的所有方面以及引导受训人员走向独立的记录。此外，候选人将 利用斯坦福大学医学院、博士后事务办公室、 和斯坦福大学NHGRI资助的中心在与领导者交流的同时获得职业发展技能 基因组学。此外，他导师实验室内的研究基础设施将使他能够有效地执行 科学目标，在这一建议所涵盖的领域接受培训，并向独立过渡。 这项工作的目标是开发单细胞基因组学方法来绘制整个体细胞进化图。 人体。最近大量测序研究的证据表明，体细胞进化发生在 几乎所有的组织，但目前的方法缺乏敏感性来解决克隆扩张，相关的细胞状态， 或者它们在全身的普遍程度。研究体细胞进化的一个关键瓶颈是 基因组学技术，如果得到解决，可能会导致对癌症等疾病的发病机制的洞察。 在目标1(K99)中，候选人将建立一种新的单细胞方法来衡量可获得性 染色质、蛋白质丰度和线粒体DNA突变以识别克隆性扩张和相关细胞 状态发生变化。在目标2(K99)中，候选人将应用多组学技术来确定来源和 巨噬细胞在人类妇科组织和肿瘤中的扩张。在过渡到教职员工之后 目标3(R00)的位置，候选人将专注于创造大规模的单细胞全基因组 与功能测量配对的测序方法，包括RNA或蛋白质定量。全 AIMS将利用和建立尖端的单细胞多组学技术来研究体细胞进化。 总而言之，对这项研究的追求将产生工具和见解，直接为物业提供信息 人体组织生理学和对年龄相关疾病的早期检测、表征和理解的帮助 疾病，包括癌症。产生的所有协议、数据、分析框架和软件工具 在本研究期间，将免费分发。总而言之，这项提案将带来对 体细胞进化的分子特征和调控，并作为一种有效的训练计划。 拉罗将以终身教职调查员的身份开始他的独立职业生涯。

PROJECT SUMMARY This proposal outlines a five-year career development program for Caleb Lareau, Ph.D. to prepare him for an independent research career in human genomics to study cellular processes underlying complex disease. The candidate will conduct his postdoctoral training at Stanford University, which provides an outstanding environment to complete the proposed research and develop skills in massive-scale computational analyses, genomics technology development, and immunology. Dr. Lareau’s mentors and advisors, including Drs. Satpathy, Kundaje, Greenleaf, Howitt, Curtis, and Anderson, have diverse technical expertise relevant to all aspects of the proposal and track records of guiding trainees to independence. Further, the candidate will utilize world-class resources available through the Stanford School of Medicine, Office of Postdoctoral Affairs, and NHGRI-funded Centers at Stanford to acquire career development skills while interfacing with leaders in genomics. Additionally, the research infrastructure within his mentors’ labs will enable him to efficiently perform the scientific aims, receive training in areas encompassed by this proposal, and transition to independence. The goal of this work is to develop single-cell genomics methods to chart somatic evolution throughout the human body. Evidence from recent bulk sequencing studies has indicated that somatic evolution occurs in almost all tissues, but current approaches lack sensitivity to resolve clonal expansions, associated cell states, or their prevalence throughout the body. A key bottleneck in studying somatic evolution has been limitations of genomics technologies, which if addressed, may lead to insights into the pathogenesis of diseases like cancer. In Aim 1 (K99), the candidate will establish a new single-cell approach for measuring accessible chromatin, protein abundance, and mitochondrial DNA mutations to identify clonal expansions and related cell state changes. In Aim 2 (K99), the candidate will apply multi-omics technologies to identify the origins and expansions of macrophages within human gynecological tissues and tumors. After transitioning to a faculty position for Aim 3 (R00), the candidate will focus his effort on creating massive-scale single-cell whole-genome sequencing methods that are paired with functional measurements, including RNA or protein quantification. All Aims will utilize and build upon cutting-edge single-cell multi-omics technologies to study somatic evolution. Together, the pursuit of this research will result in tools and insights that will directly inform properties of human tissue physiology and aid in the early detection, characterization, and understanding of age-associated diseases, including cancer. All protocols, data, analytical frameworks, and software tools that are produced during the duration of this research will be freely distributed. In total, the proposal will lead to novel insights into the molecular signatures and regulation of somatic evolution and serve as an effective training program for Dr. Lareau to launch his independent career as a tenure-track investigator.