Genetically Diverse Mouse Embryonic Stem Cells: A Platform for Cellular Systems Genetics

遗传多样性的小鼠胚胎干细胞：细胞系统遗传学平台

• 批准号: 10090033
• 负责人: Christopher Lee Baker
• 金额: $ 82.38万
• 依托单位: JACKSON LABORATORY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-03-01 至 2025-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10090033
• 关键词: Adoption; Allelic Imbalance; Biological Assay; Biology; Cell Line; Cell Shape; Cell Therapy; Cells; Chromosome Mapping; Communities; Confounding Factors (Epidemiology); Credentialing; Data; Data Analyses; Development; ES Cell Line; Environment; Exhibits; Gene Expression; Gene Frequency; Generations; Genes; Genetic; Genetic Research; Genetic Transcription; Genetic Variation; Genetic study; Genome; Genotype; Goals; Gold; Grant; Heterogeneity; Human; In Vitro; Inbred Strain; Inbred Strains Mice; Individual; Laboratory mice; Maps; Masks; Mesoderm; Modeling; Mus; Mutant Strains Mice; Online Systems; Organoids; Pathway interactions; Patients; Pharmacogenomics; Phenotype; Pilot Projects; Pluripotent Stem Cells; Population; Publishing; Quantitative Trait Loci; Regenerative Medicine; Regulator Genes; Reporting; Reproducibility; Research; Resolution; Resources; Role; Route; SNP genotyping; Sampling; Source; Structure; Sum; System; Systems Development; Testing; The Jackson Laboratory; Toxicogenomics; Validation; Variant; Visualization software; base; cell type; cohort; cost effective; data integration; design; embryonic stem cell; experimental study; gene environment interaction; genetic resource; genomic locus; human disease; human pluripotent stem cell; human stem cells; interactive tool; molecular phenotype; novel; personalized medicine; phenotypic data; pluripotency; precision medicine; predictive modeling; predictive test; response; reverse genetics; searchable database; single-cell RNA sequencing; stem cell biology; stem cells; tool; transcriptome sequencing

PROJECT SUMMARY The objective of this application is to generate a thoroughly-validated panel of genetically diverse mouse embryonic stem cells (mESC) that will enable widespread adoption of cellular systems genetics. Phenotypic variation, manifesting as heterogeneity in cell state, represents a significant challenge for realizing the full promise of individualized, cell-based therapies, regenerative medicine. But phenotypic variation in genetically diverse stem cells also presents an opportunity for the advancement of large scale, cellular screens of gene by environment interactions (e.g. pharmacogenomics, toxicogenomics). A variety of approaches are beginning to identify the networks that drive cell state transitions, but these efforts have largely focused on bulk assays, which do not provide sufficient resolution of cell state heterogeneity, and mask the contribution of underlying genetic variation on rare cell types. Moreover, genetic studies using human pluripotent stem cells are largely limited to testing common variants due to low allele frequencies and imbalanced population structure requiring prohibitively large samples and impeding identification of core regulatory networks with high power and resolution. Therefore, we currently lack a thorough understanding of the genes and mechanisms that underlie phenotypic variation in pluripotent stem cells. The Diversity Outbred (DO) mouse population at The Jackson Laboratory is genetically defined, diverse, and presents a singular, cost-effective opportunity to systematically investigate heterogeneity in mammalian pluripotency. Our pilot studies using DO mESCs establish the feasibility of identifying regulatory loci at high power and resolution, as well as networks conserved in mice and humans that regulate cell state transitions. In Aim 1, we will create a reference mapping panel of 300 DO mESC lines that will serve as a gold standard resource for cellular systems genetics. This panel will be fully credentialed and banked for broad availability through The Jackson Laboratory / Mutant Mouse Resource and Research Centers (MMRRC). In Aim 2, we will determine at the single cell level the transcriptional networks that regulate cell state transitions in vitro through the early stages of differentiation to mesoderm in a representative subset of 144 lines. In Aim 3, we will map quantitative trait loci (QTL) that underlie variation in cell state-specific gene expression and in the distribution of cell states in a population. In addition, we will build and test models based on polygenic scores that can predict differentiation propensity from genotype. Finally, a web-based searchable database of expression phenotypes and interactive tools for visualization of cell composition and eQTL will be made publicly available to support community queries and hypothesis generation. In sum, we will produce a resource of cell lines and gene expression data for the research community that will spur new discoveries in regenerative medicine, pharmacogenomics, and toxicogenomics.

项目摘要 该应用程序的目标是产生一组经过彻底验证的遗传多样性小鼠 胚胎干细胞（mESC），这将使细胞系统遗传学的广泛采用。表型 变化，表现为细胞状态的异质性，代表了实现完整的 个体化的细胞疗法和再生医学的前景但是基因上的表型变异 多样化的干细胞也为大规模的细胞基因筛选的发展提供了机会， 环境相互作用（如药物基因组学、毒理基因组学）。各种各样的方法开始 确定驱动细胞状态转换的网络，但这些努力主要集中在批量测定上， 其不提供单元状态异质性的足够分辨率，并且掩盖了底层的贡献。 遗传变异的稀有细胞类型。此外，使用人类多能干细胞的遗传研究在很大程度上是 由于低等位基因频率和不平衡的群体结构， 样本量过大，阻碍了对高功率核心监管网络的识别， 分辨率因此，我们目前缺乏对基因和机制的彻底了解， 多能干细胞的表型变异。The杰克逊的多样性远交（DO）小鼠种群 实验室是基因定义的，多样化的，并提出了一个单一的，具有成本效益的机会，系统地 研究哺乳动物多能性异质性。我们使用DO mESC的初步研究建立了 在高功率和分辨率下鉴定调控基因座的可行性，以及小鼠中保守的网络， 调节细胞状态转换的人类。在目标1中，我们将创建一个300 DO的参考映射面板 mESC系将作为细胞系统遗传学的黄金标准资源。该小组将全面 通过杰克逊实验室/突变小鼠资源获得广泛的可用性， 研究中心（MMRRC）。在目标2中，我们将在单细胞水平上确定转录网络， 在体外通过向中胚层分化的早期阶段调节细胞状态转变， 144行的代表子集。在目标3中，我们将定位数量性状基因座（QTL）， 细胞状态特异性基因表达和细胞状态在群体中的分布。此外，我们将建立 以及基于多基因得分的测试模型，其可以预测来自基因型的分化倾向。最后 基于网络的可搜索的表达表型数据库和用于细胞可视化的交互式工具 组成和eQTL将公开提供，以支持社区查询和假设 一代总之，我们将为研究提供细胞系和基因表达数据的资源 社区，将刺激再生医学，药物基因组学和毒理基因组学的新发现。