A generalizable framework for linking single-cell genomic states with cell fate outcomes in hematopoiesis

将单细胞基因组状态与造血细胞命运结果联系起来的通用框架

• 批准号: 10645197
• 负责人: H. LEIGHTON GRIMES
• 金额: $ 106.15万
• 依托单位: CINCINNATI CHILDRENS HOSP MED CTR
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-15 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10645197
• 关键词: Acceleration; Address; Adoptive Transfer; Antibodies; Architecture; Bar Codes; Biological; Biological Assay; Blood Cells; Bone Marrow; Catalogs; Cell Maturation; Cell physiology; Cell surface; Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; Chromatin; Collaborations; Colony-Forming Units Assay; Communities; Complement; Confusion; Coupled; Data Set; Development; Disease; Dissection; Elements; Enhancers; Explosion; Flow Cytometry; Gene Expression; Genes; Genetic; Genetic Transcription; Genomics; Health; Hematologist; Hematopoiesis; Hematopoietic; Hematopoietic Cell Production; Hematopoietic System; Hematopoietic stem cells; Heterogeneity; Hi-C; Human; Impairment; In Vitro; Interdisciplinary Study; Link; Macrophage; Methods; Molecular; Multipotent Stem Cells; Mus; Myelogenous; Myeloid Cells; Oligonucleotides; Outcome; Population; Production; Reporter; Sorting; Specific qualifier value; System; Systems Biology; Testing; Transplantation; Validation; Work; analytical method; bioinformatics pipeline; bioinformatics tool; computer framework; computerized tools; disorder prevention; functional genomics; gene regulatory network; genomic data; in vivo; indexing; insight; microscopic imaging; neutrophil; online resource; progenitor; programs; promoter; self-renewal; single cell technology; single-cell RNA sequencing; tool; transcription factor; transcriptome; Acceleration; Address; Adoptive Transfer; Antibodies; Architecture; Bar Codes; Biological; Biological Assay; Blood Cells; Bone Marrow; Catalogs; Cell Maturation; Cell physiology; Cell surface; Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; Chromatin; Collaborations; Colony-Forming Units Assay; Communities; Complement; Confusion; Coupled; Data Set; Development; Disease; Dissection; Elements; Enhancers; Explosion; Flow Cytometry; Gene Expression; Genes; Genetic; Genetic Transcription; Genomics; Health; Hematologist; Hematopoiesis; Hematopoietic; Hematopoietic Cell Production; Hematopoietic System; Hematopoietic stem cells; Heterogeneity; Hi-C; Human; Impairment; In Vitro; Interdisciplinary Study; Link; Macrophage; Methods; Molecular; Multipotent Stem Cells; Mus; Myelogenous; Myeloid Cells; Oligonucleotides; Outcome; Population; Production; Reporter; Sorting; Specific qualifier value; System; Systems Biology; Testing; Transplantation; Validation; Work; analytical method; bioinformatics pipeline; bioinformatics tool; computer framework; computerized tools; disorder prevention; functional genomics; gene regulatory network; genomic data; in vivo; indexing; insight; microscopic imaging; neutrophil; online resource; progenitor; programs; promoter; self-renewal; single cell technology; single-cell RNA sequencing; tool; transcription factor; transcriptome

PROJECT SUMMARY Currently, conventional methods that have been utilized to characterize hematopoietic progenitors and their potentials including flow cytometry, in vitro colony-forming-unit assays and in vivo genetic marking are being vigorously complemented with genomics analyses such as single-cell RNA-Seq (scRNA-Seq) and scATACSeq. While these complementary analyses are defining a multitude of possible cell states, there is considerable confusion concerning the correspondence between such states and the heterogeneity/identity of cells captured within canonical flow cytometry gates, their developmental potentials, and mechanisms underlying lineage specification. To address this fundamental problem in the field we have assembled an interdisciplinary research team with deep expertise in the application of single-cell technologies, hematopoiesis, computational genomics and systems biology to develop and promote a unifying framework for the analysis of genomic states with their developmental potentials and trajectories. Specifically, we will define prevalent and rare hematopoietic intermediates as well as their developmental potencies, restrictions and trajectories, on the basis of their genomic states along with the optimal markers and flow gates necessary to isolate them. Using these genomic datasets coupled with analyses of poised or active enhancers interacting with promoters, we will infer gene regulatory networks (GRNs) that delineate the connectivity of transcription factors to their target genes thereby inferring control mechanisms underlying the distinctive genomic states. Thus, exploiting a consolidated biological, molecular and computational dissection of the hematopoietic system focusing on underlying genomic regulatory architectures, we will provide a new framework to incisively understand steady state hematopoiesis.

项目摘要 当前，已用于表征造血祖细胞的常规方法及其潜力，包括流式细胞术，体外集落形成单位分析和体内遗传标记，正在与基因组学分析（如单细胞RNA-seq（SCRNA-SEPE）和ScAtaceq等基因组分析（例如基因组学分析）和体内遗传标记。尽管这些互补分析定义了许多可能的细胞态，但对于这种状态与构成流式细胞仪门内捕获的细胞的异质性/身份之间的对应关系存在相当大的混乱，其发育潜力，其发育潜力以及谱系规范规范的机制。为了解决该领域的这个基本问题，我们在应用单细胞技术，造血，计算基因组学和系统生物学的应用方面汇集了一个跨学科研究团队，以开发和促进统一的统一框架，以及其发展和轨迹分析基因组状态的统一框架。具体而言，我们将根据其基因组状态以及隔离它们所必需的最佳标记和最佳标记和流门来定义普遍且稀有的造血中间体及其发育能力，限制和轨迹。使用这些基因组数据集，再加上与启动子相互作用的固定或主动增强子的分析，我们将推断出基因调节网络（GRN），这些网络（GRN）描述了转录因子与目标基因的连通性，从而推断出独特基因组状态的控制机制。因此，利用造血系统的综合生物学，分子和计算解剖，集中于潜在的基因组调节结构，我们将提供一个新的框架，以敏锐地了解稳态造血。