Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization

Item Type:	Article
Title:	Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization
Creators Name:	Baccin, C. and Al-Sabah, J. and Velten, L. and Helbling, P.M. and Grünschläger, F. and Hernández-Malmierca, P. and Nombela-Arrieta, C. and Steinmetz, L.M. and Trumpp, A. and Haas, S.
Abstract:	The bone marrow constitutes the primary site for life-long blood production and skeletal regeneration. However, its cellular and spatial organization remains controversial. Here, we combine single-cell and spatially resolved transcriptomics to systematically map the molecular, cellular and spatial composition of distinct bone marrow niches. This allowed us to transcriptionally profile all major bone-marrow-resident cell types, determine their localization and clarify sources of pro-haematopoietic factors. Our data demonstrate that Cxcl12-abundant-reticular (CAR) cell subsets (Adipo-CAR and Osteo-CAR) differentially localize to sinusoidal and arteriolar surfaces, act locally as 'professional cytokine-secreting cells' and thereby establish peri-vascular micro-niches. Importantly, the three-dimensional bone-marrow organization can be accurately inferred from single-cell transcriptome data using the RNA-Magnet algorithm described here. Together, our study reveals the cellular and spatial organization of bone marrow niches and offers a systematic approach to dissect the complex organization of whole organs.
Keywords:	Bone Marrow, Bone Marrow Cells, Hematopoietic Stem Cells, Mesenchymal Stem Cells, Osteoblasts, Stem Cell Niche, Transcriptome, Animals
Source:	Nature Cell Biology
ISSN:	1465-7392
Publisher:	Nature Publishing Group
Volume:	22
Number:	1
Page Range:	38-48
Date:	January 2020
Official Publication:	https://doi.org/10.1038/s41556-019-0439-6
PubMed:	View item in PubMed

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