Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta

Hematopoietic stem cells (HSCs) are responsible for the production of billions of blood cells every day throughout life. In the clinic, HSC transplantations are common practice to treat patients with blood-related genetic disorders and malignancies. However, finding match donor HSCs for the increasing number of transplantations has become an issue. Intensive years of research have focused on the possibility to generate HSCs in vitrothat would serve as a potential alternative source for these life-saving cells. Unfortunately, it remains extremely difficult to achieve to date because not all steps leading to HSC generation in vivohave been elucidated yet. Without this knowledge, the in vitroproduction of HSCs will remain an important challenge.

Adult HSCs are initially generated in the main arteries (such as the aorta) during embryonic development. HSCs derive from specialized endothelial cells, located in the arteries wall and endowed with a hemogenic potential. The hemogenic endothelial (HE) cells transdifferentiate into HSC precursors (pre-HSCs) that form cell clusters. The clusters transiently remain attached to the vessels wall where pre-HSCs start to mature toward an HSC fate. The maturation process continues after migration into the fetal liver to establish the adult HSC pool that will colonize the bone marrow prior to birth. The molecular events regulating endothelial specification (to acquire a hemogenic potential), cluster formation, and their consecutive maturation into HSCs remain poorly understood. In this study, single-cell RNA-sequencing (scRNA-Seq) was performed on the successive populations leading to cluster cell formation in the mouse embryo aorta (including endothelial cells, HE cells, pre-HSCs). Data analysis revealed that the clusters are composed of pre-HSCs and few committed hematopoietic progenitors discernible by opposing gradients of endothelial and hematopoietic transcripts. The study underscored the genes and transcription factor networks activated for the silencing of the endothelial program and the initiation of the hematopoietic program. Transcriptome comparison of the clusters as a whole, according to their location inside the aorta (ventral versus dorsal side) at different time points in development, was impossible thus far. A new technique was thus developed to mechanically pick-up single pure clusters inside the aorta. scRNA-Seq revealed that clusters have similar transcriptomes, independently of their position inside the aorta.

This study provides an unprecedented complete resource for the scientific community to study in depth the molecular changes occurring in the successive steps leading to HSC formation, as it originally occurs in vivoin the aorta of the developing mouse embryo. Such knowledge will certainly help to improve the in vitroproduction of bona fideHSCs, which are in need for therapies.

ARTICLE: Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta. Chloé S. Baron*, Lennart Kester*, Anna Klaus^#, Jean-Charles Boisset^#, Roshana Thambyrajah, Laurent Yvernogeau, Valérie Kouskoff, Georges Lacaud, Alexander van Oudenaarden & Catherine Robin. 2018. Nature Communications 9:1-15. DOI: 10.1038/s41467-018-04893-3. * Co-first authors; ^#Co-second authors.

IMAGE: PROM1 expression in E11 mouse embryo aorta – Picture of intra-aortic hematopoietic cluster cells (c-kit+CD31+PROM1-) and endothelium (c-kit-CD31+PROM1+) after immunostaining of an E11 live thick embryo slice (c-kit: blue, CD31: green, PROM1: red). Image from Laurent Yvernogeau (Robin Lab).

Alexander van Oudenaarden is director and group leader at the Hubrecht Institute, professor of Quantitative Biology of Gene Regulation at the UMC Utrecht and the Faculty of Science at Utrecht University, and Oncode Investigator. His group uses a combination of experimental, computational, and theoretical approaches to quantitatively understand decision‐making in single cells, with a focus on questions in developmental and stem cell biology.

Catherine Robin is group leader at the Hubrecht Institute and is also appointed at the University Medical Center Utrecht. Her group focuses on the establishment of the hematopoietic system during embryonic development.