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

基本信息

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
项目类别：
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

项目摘要

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.

项目概要该应用程序的目的是生成经过彻底验证的遗传多样性小鼠组胚胎干细胞（mESC）将使细胞系统遗传学得到广泛采用。表型变异表现为细胞状态的异质性，是实现全面细胞状态的重大挑战。个体化、基于细胞的疗法、再生医学的承诺。但遗传上的表型变异多样化的干细胞也为大规模细胞基因筛选提供了机会环境相互作用（例如药物基因组学、毒物基因组学）。各种方法开始识别驱动细胞状态转变的网络，但这些努力主要集中在批量分析上，它不能提供细胞状态异质性的足够分辨率，并且掩盖了潜在的贡献稀有细胞类型的遗传变异。此外，使用人类多能干细胞的遗传学研究很大程度上是由于等位基因频率低且群体结构不平衡，仅限于测试常见变异样本量过大，阻碍了对高权力核心监管网络的识别解决。因此，我们目前对背后的基因和机制缺乏透彻的了解。多能干细胞的表型变异。 Jackson 的多样性远系 (DO) 小鼠种群实验室是基因定义的、多样化的，并提供了一个独特的、具有成本效益的机会来系统地研究哺乳动物多能性的异质性。我们使用 DO mESC 进行的试点研究确立了以高倍率和分辨率识别调控位点以及小鼠和小鼠中保守网络的可行性调节细胞状态转变的人类。在目标 1 中，我们将创建 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。该面板将完全通过杰克逊实验室/突变小鼠资源获得认证和存储以供广泛使用研究中心（MMRRC）。在目标 2 中，我们将在单细胞水平确定转录网络在体外调节细胞状态转变，直至分化为中胚层的早期阶段 144 行的代表性子集。在目标 3 中，我们将绘制导致变异的数量性状位点 (QTL) 细胞状态特异性基因表达和群体中细胞状态的分布。此外，我们还将建设以及基于多基因评分的测试模型，可以预测基因型的分化倾向。最后，一个基于网络的可搜索表达表型数据库和用于细胞可视化的交互式工具成分和 eQTL 将公开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资源社区将促进再生医学、药物基因组学和毒物基因组学的新发现。