Mapping cell fate flow and feedback control on vertebrate embryonic landscapes

绘制脊椎动物胚胎景观的细胞命运流和反馈控制

• 批准号: 10245930
• 负责人: Daniel E Wagner
• 金额: $ 133.05万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-23 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10245930
• 关键词: Address; Adult; Behavior; Biological; Cell Fate Control; Cells; Cessation of life; Complex; Computational Biology; Conceptions; Congenital Abnormality; Defect; Development; Developmental Biology; Disease; Elements; Embryo; Embryonic Development; Face; Failure; Feedback; Genes; Genetic; Genetic Models; Genome; Genomics; Growth; Health; Human; Individual; Laboratories; Lead; Life; Link; Measurement; Microfluidics; Modeling; Molecular; Molecular Genetics; Motivation; Patients; Pattern; Phenotype; Pregnancy; Process; Research; Resolution; Spontaneous abortion; System; Testing; Tissues; Vertebrates; Vision; Work; Zebrafish; assault; cell type; developmental disease; embryo tissue; experimental study; fitness; in vivo; insight; molecular decomposition; mutant; premature; programs; transcriptome; whole genome

PROJECT SUMMARY From the moment of conception until death, metazoans face relentless assault on their tissues, their cells, and their genomes. The ability of intricately patterned biological tissues to dynamically withstand these challenges is essential for adult life but is tested first – and perhaps most critically – during embryonic development. Early failures of embryonic patterning can lead to rapid and premature lethality, long-lasting birth defects, and/or devastating developmental disorders. Over the years, developmental biologists have made great progress in understanding many of the links connecting environmental and genetic perturbations to their consequences in embryos, generally by applying reductionist approaches (e.g. single-gene mutant phenotypes, single-clone fate mapping). However, a significant proportion of human pregnancies still result in developmental defects or miscarriages of unknown cause. At present, we also often fail to understand why certain perturbations result in failed embryogenesis in some individuals, but not in others. One persisting challenge is that any model of developmental patterning must simultaneously take into account many elements of a complex system: multiple cell types, each exerting both intrinsic and non-autonomous behaviors, cell turnover dynamics, lineage relationships, and many hundreds of genetic factors. To address these challenges, we are establishing a new experimental paradigm for studies of developmental biology that leverages microfluidics, single-cell genomics, computational biology, and a powerful in vivo molecular genetic model of vertebrate embryogenesis, the laboratory zebrafish (Danio rerio). Under this paradigm, we seek a new form of biological reductionism: comprehensive, molecular decomposition of vertebrate embryonic tissues into their constituent cell states, at an experimental scale not previously accessible to developmental biologists (e.g. 104–106 single-cell measurements per experiment, combined with whole-genome or whole-transcriptome resolution). In this application, we present our motivation and our vision for the whole-embryo single-cell state landscape as a versatile experimental and conceptual platform for systems- level interrogation of vertebrate embryogenesis. Using this landscape approach, we will systematically quantify developmental robustness (i.e. “canalization”) of all embryonic tissues to identify reoccurring bottlenecks and vulnerabilities that drive human birth defects. In parallel, we will dissect mechanisms for cell fate control that direct the “flow” of cells down the embryonic landscape, particularly in contexts where individual cells differ in their genetic and/or developmental fitness. Our experimental vision will therefore revisit fundamental questions in developmental biology, formulated nearly 8 decades ago, but which have persisted until now as abstract principles rather than as testable hypotheses. We anticipate this research program will accelerate our collective efforts to better understand organizing principles of developmental ontogeny in vertebrates in health and disease.

项目总结 从受孕的那一刻到死亡，后生动物面临着对它们的组织、细胞和 基因组。复杂图案的生物组织动态承受这些挑战的能力是必不可少的。 但首先是在胚胎发育期间进行测试，也许是最关键的。早期的故障 胚胎模式可能会导致快速和过早的死亡、长期的出生缺陷和/或毁灭性的 发育障碍。多年来，发育生物学家在理解 许多将环境和遗传扰动与它们在胚胎中的后果联系起来的联系，通常 通过应用简化论方法(例如，单基因突变表型、单克隆命运图谱)。然而，a 相当大比例的人类怀孕仍然会导致发育缺陷或原因不明的流产。 目前，我们也常常不能理解为什么某些扰动会导致某些胚胎发生失败。 个人，但在其他人身上不是。一个挥之不去的挑战是，任何发展模式都必须 同时考虑复杂系统的许多元素：多种细胞类型，每种细胞类型都发挥着 固有的和非自主的行为、细胞周转动态、血统关系以及数百种 遗传因素。 为了应对这些挑战，我们正在建立一种新的实验范式来研究 发育生物学，利用微流体、单细胞基因组学、计算生物学和强大的 脊椎动物胚胎发生的活体分子遗传学模型，实验室斑马鱼(Danio Rerio)。在这下面 范式，我们寻求一种新的生物还原论形式：全面的，分子分解的 脊椎动物胚胎组织进入它们的组成细胞状态，在实验规模上，而不是以前 可供发育生物学家使用(例如，每个实验104-106个单细胞测量，结合 全基因组或全转录组解析)。在此应用程序中，我们展示了我们的动机和愿景 作为系统的多功能实验和概念平台的全胚胎单细胞状态图景- 脊椎动物胚胎发生的水平询问。使用这种景观方法，我们将系统地量化 所有胚胎组织的发育稳健性(即“通道化”)，以确定复发的瓶颈和 导致人类先天缺陷的脆弱性。同时，我们将剖析细胞命运控制的机制 引导细胞“流向”胚胎，特别是在单个细胞不同的环境中。 遗传和/或发育适合性。因此，我们的实验愿景将重新审视 发育生物学，近80年前提出的，但至今仍作为抽象原理存在 而不是作为可检验的假设。我们预计这项研究计划将加快我们的集体努力 在健康和疾病中更好地理解脊椎动物发育个体发育的组织原理。