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

• Published in: Stem cell reports Vol. 14; no. 5; pp. 956 - 971
• Main Authors: Chen, Michael J., Lummertz da Rocha, Edroaldo, Cahan, Patrick, Kubaczka, Caroline, Hunter, Phoebe, Sousa, Patricia, Mullin, Nathaniel K., Fujiwara, Yuko, Nguyen, Minh, Tan, Yuqi, Landry, Samuel, Han, Areum, Yang, Song, Lu, Yi-Fen, Jha, Deepak Kumar, Vo, Linda T., Zhou, Yi, North, Trista E., Zon, Leonard I., Daley, George Q., Schlaeger, Thorsten M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 12.05.2020; Elsevier
• Subjects: Animals; Antigens, Ly - genetics; Antigens, Ly - metabolism; Cells, Cultured; Core Binding Factor Alpha 2 Subunit - genetics; development; EHT; Endothelial Progenitor Cells - cytology; Endothelial Progenitor Cells - metabolism; endothelial-to-hematopoietic transition; Genes, Reporter; Green Fluorescent Proteins - genetics; Green Fluorescent Proteins - metabolism; Hematopoiesis; hematopoietic stem cells; Hematopoietic Stem Cells - cytology; Hematopoietic Stem Cells - metabolism; hemogenic endothelial cells; Membrane Proteins - genetics; Membrane Proteins - metabolism; Mice; pre-HSCs; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; reporter; Resource; RNA-Seq; scRNA-seq; Single-Cell Analysis; Transcriptome; transcriptomics; EHT; hemogenic endothelial cells; development; scRNA-seq; endothelial-to-hematopoietic transition; transcriptomics; reporter; pre-HSCs; hematopoietic stem cells
• ISSN: 2213-6711; 2213-6711
• DOI: 10.1016/j.stemcr.2020.03.020

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. •A Runx1 and Ly6a dual reporter system identifies intra-arterial HECs•Lymphoid and HSC potential is restricted to dual reporter double-positive cells•The placenta is the first major niche for HSC maturation and expansion•Single-cell RNA-seq analyses reveal early acquisition of a quiescent HSC phenotype Chen and colleagues generate a Runx1 and Ly6a dual reporter mouse that marks pre-HSCs from specification of hemogenic endothelial cells to their migration to placenta, where they mature and expand, before colonization of the fetal liver as mature HSCs. Single-cell RNA-seq analyses of maturing HSCs reveal progressive acquisition of a quiescent state reminiscent of adult bone marrow long-term repopulating HSCs.