Transcriptome Dynamics of Hematopoietic Stem Cell Formation Revealed Using a Combinatorial Runx1 and Ly6a Reporter System

Stem Cell Reports. 2020 May 12;14(5):956-971. doi: 10.1016/j.stemcr.2020.03.020. Epub 2020 Apr 16.


Studies of hematopoietic stem cell (HSC) development from pre-HSC-producing hemogenic endothelial cells (HECs) are hampered by the rarity of these cells and the presence of other cell types with overlapping marker expression profiles. We generated a Tg(Runx1-mKO2; Ly6a-GFP) dual reporter mouse to visualize hematopoietic commitment and study pre-HSC emergence and maturation. Runx1-mKO2 marked all intra-arterial HECs and hematopoietic cluster cells (HCCs), including pre-HSCs, myeloid- and lymphoid progenitors, and HSCs themselves. However, HSC and lymphoid potential were almost exclusively found in reporter double-positive (DP) cells. Robust HSC activity was first detected in DP cells of the placenta, reflecting the importance of this niche for (pre-)HSC maturation and expansion before the fetal liver stage. A time course analysis by single-cell RNA sequencing revealed that as pre-HSCs mature into fetal liver stage HSCs, they show signs of interferon exposure, exhibit signatures of multi-lineage differentiation gene expression, and develop a prolonged cell cycle reminiscent of quiescent adult HSCs.

Keywords: EHT; development; endothelial-to-hematopoietic transition; hematopoietic stem cells; hemogenic endothelial cells; pre-HSCs; reporter; scRNA-seq; transcriptomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antigens, Ly / genetics*
  • Antigens, Ly / metabolism
  • Cells, Cultured
  • Core Binding Factor Alpha 2 Subunit / genetics*
  • Endothelial Progenitor Cells / cytology
  • Endothelial Progenitor Cells / metabolism
  • Genes, Reporter*
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism
  • Hematopoiesis*
  • Hematopoietic Stem Cells / cytology
  • Hematopoietic Stem Cells / metabolism*
  • Membrane Proteins / genetics*
  • Membrane Proteins / metabolism
  • Mice
  • RNA-Seq
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Single-Cell Analysis
  • Transcriptome*


  • Antigens, Ly
  • Core Binding Factor Alpha 2 Subunit
  • Ly6a protein, mouse
  • Membrane Proteins
  • Recombinant Proteins
  • Runx1 protein, mouse
  • Green Fluorescent Proteins