The Transcriptional Landscape of Hematopoietic Stem Cell Ontogeny

Transcriptome analysis of adult hematopoietic stem cells (HSCs) and their progeny has revealed mechanisms of blood differentiation and leukemogenesis, but a similar analysis of HSC development is lacking. Here, we acquired the transcriptomes of developing HSCs purified from >2,500 murine embryos and adult mice. We found that embryonic hematopoietic elements clustered into three distinct transcriptional states characteristic of the definitive yolk sac, HSCs undergoing specification, and definitive HSCs. We applied a network-biology-based analysis to reconstruct the gene regulatory networks of sequential stages of HSC development and functionally validated candidate transcriptional regulators of HSC ontogeny by morpholino-mediated knockdown in zebrafish embryos. Moreover, we found that HSCs from in vitro differentiated embryonic stem cells closely resemble definitive HSCs, yet lack a Notch-signaling signature, likely accounting for their defective lymphopoiesis. Our analysis and web resource will enhance efforts to identify regulators of HSC ontogeny and facilitate the engineering of hematopoietic specification. [Display omitted] ► Gene expression profiling of hematopoietic stem cells during embryonic development ► Expression profiles used to construct gene regulatory networks ► Multiple regulators of HSC development implicated ► ESC-derived HSCs resemble definitive HSCs but lack a Notch-signaling signature Network-based analysis of HSC development using transcriptome profiling reveals stage-specific developmental regulators and differences relative to HSCs derived from ESCs.