Engineering a niche supporting hematopoietic stem cell development using integrated single-cell transcriptomics

Brandon Hadland (), Barbara Varnum-Finney, Stacey Dozono, Tessa Dignum, Cynthia Nourigat-McKay, Adam M. Heck, Takashi Ishida, Dana L. Jackson, Tomer Itkin, Jason M. Butler, Shahin Rafii, Cole Trapnell and Irwin D. Bernstein
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Brandon Hadland: Clinical Research Division, Fred Hutchinson Cancer Research Center
Barbara Varnum-Finney: Clinical Research Division, Fred Hutchinson Cancer Research Center
Stacey Dozono: Clinical Research Division, Fred Hutchinson Cancer Research Center
Tessa Dignum: Clinical Research Division, Fred Hutchinson Cancer Research Center
Cynthia Nourigat-McKay: Clinical Research Division, Fred Hutchinson Cancer Research Center
Adam M. Heck: Clinical Research Division, Fred Hutchinson Cancer Research Center
Takashi Ishida: Clinical Research Division, Fred Hutchinson Cancer Research Center
Dana L. Jackson: University of Washington School of Medicine
Tomer Itkin: Department of Genetic Medicine, Ansary Stem Cell Institute, Howard Hughes Medical Institute, Weill Cornell Medical College
Jason M. Butler: Hackensack University Medical Center
Shahin Rafii: Department of Genetic Medicine, Ansary Stem Cell Institute, Howard Hughes Medical Institute, Weill Cornell Medical College
Cole Trapnell: University of Washington School of Medicine
Irwin D. Bernstein: Clinical Research Division, Fred Hutchinson Cancer Research Center

Nature Communications, 2022, vol. 13, issue 1, 1-17

Abstract: Abstract Hematopoietic stem cells (HSCs) develop from hemogenic endothelium within embryonic arterial vessels such as the aorta of the aorta-gonad-mesonephros region (AGM). To identify the signals responsible for HSC formation, here we use single cell RNA-sequencing to simultaneously analyze the transcriptional profiles of AGM-derived cells transitioning from hemogenic endothelium to HSCs, and AGM-derived endothelial cells which provide signals sufficient to support HSC maturation and self-renewal. Pseudotemporal ordering reveals dynamics of gene expression during the hemogenic endothelium to HSC transition, identifying surface receptors specifically expressed on developing HSCs. Transcriptional profiling of niche endothelial cells identifies corresponding ligands, including those signaling to Notch receptors, VLA-4 integrin, and CXCR4, which, when integrated in an engineered platform, are sufficient to support the generation of engrafting HSCs. These studies provide a transcriptional map of the signaling interactions necessary for the development of HSCs and advance the goal of engineering HSCs for therapeutic applications.

Date: 2022
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DOI: 10.1038/s41467-022-28781-z

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