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 该应用的目的是生成彻底验证的遗传多样的小鼠面板 胚胎干细胞（MESC），可以广泛采用细胞系统遗传学。表型 变异，表现为细胞状态的异质性，代表了实现完整的重大挑战 对个性化的，基于细胞的疗法的承诺，再生医学。但是遗传上的表型变异 多样的干细胞还为大规模发展基因细胞筛选的机会提供了机会 环境相互作用（例如，药物基因组学，毒理基因组学）。各种方法开始 确定推动细胞状态过渡的网络，但这些努力主要集中在批量测定上， 它不能提供足够的细胞状态异质性的分辨率，并掩盖了基础的贡献 稀有细胞类型的遗传变异。此外，使用人多能干细胞的遗传研究在很大程度上是 由于等位基因频率较低和种群结构不平衡，仅限于测试常见变体 大型样本和阻碍具有高功率和 解决。因此，我们目前对基因和机制缺乏透彻的理解 多能干细胞的表型变异。杰克逊的多样性杂种（do）鼠标 实验室是基因定义的，多样的，并且为系统地提供了一个单一的，具有成本效益的机会 研究哺乳动物多能性的异质性。我们使用DO MESC的试点研究建立了 在高功率和解决方案中识别监管基因座的可行性，以及在小鼠中保守的网络 调节细胞状态过渡的人类。在AIM 1中，我们将创建一个300的参考映射面板 MESC线将作为细胞系统遗传学的黄金标准资源。这个面板将完全 通过杰克逊实验室 /突变鼠标资源和 研究中心（MMRRC）。在AIM 2中，我们将在单个单元格级别确定转录网络 通过分化与中胚层的早期阶段，在体外调节细胞状态过渡 144行的代表性子集。在AIM 3中，我们将绘制基于变化的定量性状基因座（QTL） 细胞态特异性基因表达和人群中细胞态的分布。此外，我们将建造 基于可以预测基因型分化倾向的多基因评分的测试模型。最后，一个 基于Web的表达表型和可视化单元可视化的交互式工具的可搜索数据库 组成和EQTL将公开使用以支持社区查询和假设 一代。总而言之，我们将为研究生成细胞系和基因表达数据的资源 将刺激新发现的新发现，药物基因组学和毒理基因组学的社区。