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

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

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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。