JAX MorPhiC Data Production Center

JAX MorPhiC 数据生产中心

基本信息

批准号：
10676998
负责人：
Paul Robson
金额：
$ 191.28万
依托单位：
JACKSON LABORATORY
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-08-04 至 2027-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10676998
关键词：
Accountability Address Administrative Coordination Affect Alleles Archives Biological Biological Assay Biological Process Catalogs Cell Line Cell Lineage Cell Nucleus Cells Clone Cells Code Communication Communities Data Development Developmental Biology Disease Doctor of Philosophy Elderly Embryo Endocrine Engineering Ensure Essential Genes Excision Exhibits Exons Future Gene Deletion Generations Genes Genetic Genetic Transcription Genomic medicine Giant Cells Goals Human Image Infrastructure Invaded Knock-out Knockout Mice Knowledge Leadership Mediating Methods Micronutrients Molecular Morphology Mutation Neurodevelopmental Disorder Nucleic Acid Regulatory Sequences Nutrient Pathway interactions Phase Phenotype Primates Process Production Proteins Protocols documentation Regulatory Element Research Resolution Resources Role Scheme Scientist Selection Criteria Specificity Structure System Technology Terminator Codon The Jackson Laboratory Time Work cell type cellular engineering data dissemination data management data resource epigenomics experience genome-wide human disease immunoregulation induced pluripotent stem cell innovation insight knockout gene lipidomics loss of function mutation meetings metabolomics molecular phenotype mutant null mutation pleiotropism premature programs research and development response scientific organization sex single cell analysis skills stem cell biology stem cell differentiation tool transcription factor transcriptomics uptake wasting

项目摘要

PROJECT SUMMARY This proposal will establish a Molecular Phenotypes of Null Alleles in Cells (MorPhiC) Phase 1: Data Production Research and Development Center based entirely at The Jackson Laboratory for Genomic Medicine – the JAX MorPhiC Center. JAX MorPhiC will comprise, under one roof, a team of highly collaborative scientists with complementary skill sets and decades of cumulative experience in mammalian gene knockouts (KO), stem cell and developmental biology, molecular phenotyping, single cell analysis, and advanced metabolomics and lipidomics capabilities. We will KO 250 protein-coding genes over the Phase 1 period of this initiative and will engineer these KOs in human induced pluripotent stem cells (iPSCs) that will subsequently be differentiated into two cell lineages, the extra-embryonic and the neuroectodermal, where cells will then be comprehensively phenotyped. Our rationale for selecting these lineages is that they are two of the most evolutionary divergent between species, and primate-specificity is one of our criteria for gene prioritization. In addition, the extra- embryonic lineage rapidly develops into a cellular functional endpoint responsible for many biological processes, thus permitting interpretation of function of diverse genes, whereas the early neuroectodermal lineage is relevant to neurodevelopmental disorders. In Aim 1, we will prioritize genes for knockout; selection criteria include expression in extra-embryonic or neuroectodermal lineages, primate-specific features, broad classes of functions while enriching for transcription factors, and genes implicated in human disease. In Aim 2, we will generate iPSC KO clones in high-throughput using high-efficiency protocols and workflows established in JAX's Cellular Engineering core. We will engineer KO clones for 250 genes in the well-characterized, stable human iPSC line, KOLF2.1, while considering the effects of sex, genetic background, possible adaptive/compensatory responses, and different KO strategies including incorporation of conditional/reversible and scalable approaches. In Aim 3, will carry out comprehensive phenotyping of derivatives differentiated from KO iPSCs. We have selected a combination of assays to maximally integrate consistency, scalability, and functional informativeness to help achieve the overall objectives of the MorPhiC Consortium. These include imaging, single cell transcriptomics, single nucleus epigenomics, and metabolomics/lipidomics. Our research Aims will be coordinated in administrative Aim 4, which will ensure efficient project management and oversight, internal and external communications, and data dissemination to the MorPhiC Data Resource and Administrative Coordination Center (DRACC). Successful completion of the proposed work will address several main barriers hampering the ultimate goal of the MorPhiC Consortium to functionally characterize all human genes: identifying the most effective KO strategies and optimal phenotyping technologies, as well as scaling efficiencies to expand this program towards future MorPhiC Phases. In the process, we will generate a valuable resource of 250 human iPSC KO lines that will be distributed to the scientific community via existing operational infrastructure at JAX.

项目概要该提案将建立细胞中无效等位基因的分子表型 (MorPhiC) 第一阶段：数据生产完全位于杰克逊基因组医学实验室的研发中心 – JAX MorPhiC 中心 JAX MorPhiC 将由一支高度协作的科学家团队组成，在哺乳动物基因敲除 (KO)、干细胞方面互补的技能和数十年的累积经验和发育生物学、分子表型、单细胞分析和先进的代谢组学和我们将在该计划的第一阶段消除 250 个蛋白质编码基因。在人类诱导多能干细胞 (iPSC) 中设计这些 KO，这些细胞随后将分化为两种细胞谱系，胚胎外细胞和神经外胚层细胞，然后细胞将被全面分类我们选择这些谱系的理由是它们是进化上差异最大的两个谱系。物种之间的差异，灵长类动物的特异性是我们基因优先排序的标准之一。胚胎谱系迅速发展成为负责许多生物过程的细胞功能终点，因此可以解释不同基因的功能，而早期神经外胚层谱系是相关的在目标 1 中，我们将优先考虑基因敲除的选择标准：在胚胎外或神经外胚层谱系中的表达、灵长类特异性特征、广泛的类别在目标 2 中，我们将富集转录因子和与人类疾病有关的基因。使用 JAX 中建立的高效协议和工作流程以高通量生成 iPSC KO 克隆细胞工程核心。我们将在特征明确、稳定的人类体内对 250 个基因进行 KO 克隆。 iPSC系，KOLF2.1，同时考虑性别、遗传背景、可能的适应性/补偿的影响响应，以及不同的 KO 策略，包括结合条件/可逆和可扩展的方法。在目标 3 中，将对 KO iPSC 分化的衍生物进行全面的表型分析。选择了多种检测方法的组合，以最大程度地整合一致性、可扩展性和功能信息性帮助实现 MorPhiC 联盟的总体目标，其中包括成像、单细胞。我们的研究目标是转录组学、单核表观基因组学和代谢组学/脂质组学。在行政目标 4 中进行协调，这将确保内部和外部高效的项目管理和监督外部通信以及向 MorPhiC 数据资源和管理的数据传播协调中心（DRACC）的成功完成拟议工作将解决几个主要障碍。阻碍了 MorPhiC 联盟从功能上表征所有人类基因的最终目标：识别最有效的 KO 策略和最佳表型分析技术，以及扩展效率该计划未来将走向 MorPhiC 阶段。在此过程中，我们将产生 250 名宝贵的人力资源。 iPSC KO 系列将通过 JAX 现有的运营基础设施分发给科学界。