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

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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.