Journal Article

DKFZ-2020-00020

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization.

Baccin, C. ; Al-Sabah, J. (First author)DKFZ* ; Velten, L. ; Helbling, P. M. ; Grünschläger, F.DKFZ* ; Hernández-Malmierca, P.DKFZ* ; Nombela-Arrieta, C. ; Steinmetz, L. M. ; Trumpp, A. (Last author)DKFZ* ; Haas, S. (Last author)DKFZ*

2020
Nature America New York, NY

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Please use a persistent id in citations: doi:10.1038/s41556-019-0439-6

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.

Note: DKFZ-ZMBH Alliance2020 Jan;22(1):38-48#LA:A010#

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Contributing Institute(s):

1. A010 Stammzellen und Krebs (A010)
2. V960 HI-Stem (V960)
3. DKTK HD zentral (HD01)

Research Program(s):

1. 311 - Signalling pathways, cell and tumor biology (POF3-311) (POF3-311)

Appears in the scientific report 2020

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Database coverage:
; BIOSIS Previews ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; Ebsco Academic Search ; IF >= 15 ; JCR ; NCBI Molecular Biology Database ; Nationallizenz ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Web of Science Core Collection

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