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

项目摘要 目前，已经用于表征造血祖细胞及其潜力的常规方法，包括流式细胞术、体外集落形成单位测定和体内遗传标记，正在大力补充基因组学分析，如单细胞RNA-Seq（scRNA-Seq）和scATACSeq。虽然这些补充分析定义了多种可能的细胞状态，但关于这些状态与在规范流式细胞术门内捕获的细胞的异质性/身份之间的对应关系、其发育潜力和谱系特化的机制存在相当大的混淆。为了解决这一领域的基本问题，我们组建了一个跨学科的研究团队，在单细胞技术，造血，计算基因组学和系统生物学的应用方面具有深厚的专业知识，以开发和促进一个统一的框架，用于分析基因组状态及其发展潜力和轨迹。具体来说，我们将定义普遍和罕见的造血中间体，以及他们的发展潜力，限制和轨迹，其基因组状态的基础上，沿着的最佳标记和必要的分离它们的流动门。使用这些基因组数据集，再加上与启动子相互作用的平衡或活性增强子的分析，我们将推断出基因调控网络（GRNs），该网络描绘了转录因子与其靶基因的连接性，从而推断出独特的基因组状态下的控制机制。因此，利用巩固的生物，分子和计算解剖造血系统的基础基因组调控架构，我们将提供一个新的框架，深刻理解稳态造血。

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.