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

项目总结 目前，已用于表征造血祖细胞及其潜能的常规方法包括流式细胞术、体外集落形成单位分析和体内遗传标记，并正在与基因组学分析如单细胞RNA-Seq(scRNA-Seq)和scATACSeq进行强有力的补充。虽然这些互补的分析定义了许多可能的细胞状态，但对于这些状态与规范的流式细胞术门内捕获的细胞的异质性/同一性之间的对应关系、它们的发育潜力以及潜在的谱系指定机制，仍存在相当大的混乱。为了解决这一领域的根本问题，我们组建了一个在单细胞技术、造血、计算基因组学和系统生物学应用方面拥有深厚专业知识的跨学科研究团队，以开发和促进分析基因组状态及其发展潜力和轨迹的统一框架。具体地说，我们将根据它们的基因组状态以及分离它们所需的最佳标记和流门，定义普遍和罕见的造血中间体及其发育潜力、限制和轨迹。利用这些基因组数据集，结合对稳定的或活性的增强子与启动子相互作用的分析，我们将推断基因调控网络(GRN)，该网络描述了转录因子与其靶基因的连接，从而推断出潜在的不同基因组状态的控制机制。因此，利用对造血系统的生物学、分子和计算方面的综合剖析，我们将提供一个新的框架来深入了解稳态造血。

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.