The bone marrow microenvironment at single-cell resolution.
Adaptor Proteins, Signal Transducing
/ metabolism
Adipocytes
/ cytology
Animals
Bone Marrow
/ blood supply
Calcium-Binding Proteins
/ metabolism
Cell Differentiation
Cell Lineage
Cellular Microenvironment
Endothelium, Vascular
/ cytology
Female
Gene Expression Regulation
Hematopoiesis
/ genetics
Hematopoietic Stem Cells
/ cytology
Male
Mice
Myeloid Cells
/ cytology
Osteoblasts
/ cytology
RNA-Seq
Receptors, Notch
/ metabolism
Single-Cell Analysis
Stem Cell Niche
/ genetics
Stress, Physiological
/ genetics
Transcriptome
/ genetics
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
05 2019
05 2019
Historique:
received:
14
12
2017
accepted:
13
03
2019
pubmed:
12
4
2019
medline:
18
12
2019
entrez:
12
4
2019
Statut:
ppublish
Résumé
The bone marrow microenvironment has a key role in regulating haematopoiesis, but its molecular complexity and response to stress are incompletely understood. Here we map the transcriptional landscape of mouse bone marrow vascular, perivascular and osteoblast cell populations at single-cell resolution, both at homeostasis and under conditions of stress-induced haematopoiesis. This analysis revealed previously unappreciated levels of cellular heterogeneity within the bone marrow niche and resolved cellular sources of pro-haematopoietic growth factors, chemokines and membrane-bound ligands. Our studies demonstrate a considerable transcriptional remodelling of niche elements under stress conditions, including an adipocytic skewing of perivascular cells. Among the stress-induced changes, we observed that vascular Notch delta-like ligands (encoded by Dll1 and Dll4) were downregulated. In the absence of vascular Dll4, haematopoietic stem cells prematurely induced a myeloid transcriptional program. These findings refine our understanding of the cellular architecture of the bone marrow niche, reveal a dynamic and heterogeneous molecular landscape that is highly sensitive to stress and illustrate the utility of single-cell transcriptomic data in evaluating the regulation of haematopoiesis by discrete niche populations.
Identifiants
pubmed: 30971824
doi: 10.1038/s41586-019-1104-8
pii: 10.1038/s41586-019-1104-8
pmc: PMC6607432
mid: NIHMS1023835
doi:
Substances chimiques
Adaptor Proteins, Signal Transducing
0
Calcium-Binding Proteins
0
DLL4 protein, mouse
0
Dlk1 protein, mouse
0
Receptors, Notch
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
222-228Subventions
Organisme : NIDDK NIH HHS
ID : R01 DK112976
Pays : United States
Organisme : European Research Council
Pays : International
Organisme : NHLBI NIH HHS
ID : R01 HL069438
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA105129
Pays : United States
Organisme : NHGRI NIH HHS
ID : DP2 HG009623
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA202025
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA169784
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL130937
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK056638
Pays : United States
Organisme : NIDDK NIH HHS
ID : U01 DK116312
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA194923
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA202027
Pays : United States
Commentaires et corrections
Type : ErratumIn
Références
Morrison, S. J. & Scadden, D. T. The bone marrow niche for haematopoietic stem cells. Nature 505, 327–334 (2014).
doi: 10.1038/nature12984
Wei, Q. & Frenette, P. S. Niches for hematopoietic stem cells and their progeny. Immunity 48, 632–648 (2018).
doi: 10.1016/j.immuni.2018.03.024
Ding, L. & Morrison, S. J. Haematopoietic stem cells and early lymphoid progenitors occupy distinct bone marrow niches. Nature 495, 231–235 (2013).
doi: 10.1038/nature11885
Zhu, J. et al. Osteoblasts support B-lymphocyte commitment and differentiation from hematopoietic stem cells. Blood 109, 3706–3712 (2007).
doi: 10.1182/blood-2006-08-041384
Méndez-Ferrer, S., Lucas, D., Battista, M. & Frenette, P. S. Haematopoietic stem cell release is regulated by circadian oscillations. Nature 452, 442–447 (2008).
doi: 10.1038/nature06685
Lucas, D. et al. Chemotherapy-induced bone marrow nerve injury impairs hematopoietic regeneration. Nat. Med. 19, 695–703 (2013).
doi: 10.1038/nm.3155
Chow, A. et al. Bone marrow CD169
doi: 10.1084/jem.20101688
Bruns, I. et al. Megakaryocytes regulate hematopoietic stem cell quiescence through CXCL4 secretion. Nat. Med. 20, 1315–1320 (2014).
doi: 10.1038/nm.3707
Yamazaki, S. et al. Nonmyelinating Schwann cells maintain hematopoietic stem cell hibernation in the bone marrow niche. Cell 147, 1146–1158 (2011).
doi: 10.1016/j.cell.2011.09.053
Kusumbe, A. P., Ramasamy, S. K. & Adams, R. H. Coupling of angiogenesis and osteogenesis by a specific vessel subtype in bone. Nature 507, 323–328 (2014).
doi: 10.1038/nature13145
Zhou, B. O., Yue, R., Murphy, M. M., Peyer, J. G. & Morrison, S. J. Leptin-receptor-expressing mesenchymal stromal cells represent the main source of bone formed by adult bone marrow. Cell Stem Cell 15, 154–168 (2014).
doi: 10.1016/j.stem.2014.06.008
Mizoguchi, T. et al. Osterix marks distinct waves of primitive and definitive stromal progenitors during bone marrow development. Dev. Cell 29, 340–349 (2014).
doi: 10.1016/j.devcel.2014.03.013
Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411–420 (2018).
doi: 10.1038/nbt.4096
Ramasamy, S. K. Structure and functions of blood vessels and vascular niches in bone. Stem Cells Int. 2017, 5046953 (2017).
doi: 10.1155/2017/5046953
Xu, C. et al. Stem cell factor is selectively secreted by arterial endothelial cells in bone marrow. Nat. Commun. 9, 2449 (2018).
doi: 10.1038/s41467-018-04726-3
Hooper, A. T. et al. Engraftment and reconstitution of hematopoiesis is dependent on VEGFR2-mediated regeneration of sinusoidal endothelial cells. Cell Stem Cell 4, 263–274 (2009).
doi: 10.1016/j.stem.2009.01.006
Nombela-Arrieta, C. et al. Quantitative imaging of haematopoietic stem and progenitor cell localization and hypoxic status in the bone marrow microenvironment. Nat. Cell Biol. 15, 533–543 (2013).
doi: 10.1038/ncb2730
Crane, G. M., Jeffery, E. & Morrison, S. J. Adult haematopoietic stem cell niches. Nat. Rev. Immunol. 17, 573–590 (2017).
doi: 10.1097/00007890-196803000-00009
Ghazanfari, R., Li, H., Zacharaki, D., Lim, H. C. & Scheding, S. Human non-hematopoietic CD271
doi: 10.1089/scd.2016.0169
Mitroulis, I. et al. Secreted protein Del-1 regulates myelopoiesis in the hematopoietic stem cell niche. J. Clin. Invest. 127, 3624–3639 (2017).
doi: 10.1172/JCI92571
Yang, G. et al. Osteogenic fate of hypertrophic chondrocytes. Cell Res. 24, 1266–1269 (2014).
doi: 10.1038/cr.2014.111
Winkler, I. G. et al. Vascular niche E-selectin regulates hematopoietic stem cell dormancy, self renewal and chemoresistance. Nat. Med. 18, 1651–1657 (2012).
doi: 10.1038/nm.2969
Cordeiro Gomes, A. et al. Hematopoietic stem cell niches produce lineage-instructive signals to control multipotent progenitor differentiation. Immunity 45, 1219–1231 (2016).
doi: 10.1016/j.immuni.2016.11.004
Mrózek, E., Anderson, P. & Caligiuri, M. A. Role of interleukin-15 in the development of human CD56
pubmed: 8639878
Goldman, D. C. et al. BMP4 regulates the hematopoietic stem cell niche. Blood 114, 4393–4401 (2009).
doi: 10.1182/blood-2009-02-206433
Shi, C. et al. Bone marrow mesenchymal stem and progenitor cells induce monocyte emigration in response to circulating Toll-like receptor ligands. Immunity 34, 590–601 (2011).
doi: 10.1016/j.immuni.2011.02.016
Nemeth, M. J., Topol, L., Anderson, S. M., Yang, Y. & Bodine, D. M. Wnt5a inhibits canonical Wnt signaling in hematopoietic stem cells and enhances repopulation. Proc. Natl Acad. Sci. USA 104, 15436–15441 (2007).
doi: 10.1073/pnas.0704747104
Smith, G. D., Gunnell, D. & Holly, J. Cancer and insulin-like growth factor-I. BMJ 321, 847–848 (2000).
doi: 10.1136/bmj.321.7265.847
Yu, V. W. et al. Distinctive mesenchymal–parenchymal cell pairings govern B cell differentiation in the bone marrow. Stem Cell Reports 7, 220–235 (2016).
doi: 10.1016/j.stemcr.2016.06.009
Mauch, P. et al. Hematopoietic stem cell compartment: acute and late effects of radiation therapy and chemotherapy. Int. J. Radiat. Oncol. Biol. Phys. 31, 1319–1339 (1995).
doi: 10.1016/0360-3016(94)00430-S
Hérault, A. et al. Myeloid progenitor cluster formation drives emergency and leukaemic myelopoiesis. Nature 544, 53–58 (2017).
doi: 10.1038/nature21693
Zhou, B. O. et al. Bone marrow adipocytes promote the regeneration of stem cells and haematopoiesis by secreting SCF. Nat. Cell Biol. 19, 891–903 (2017).
doi: 10.1038/ncb3570
Van Zant, G. Studies of hematopoietic stem cells spared by 5-fluorouracil. J. Exp. Med. 159, 679–690 (1984).
doi: 10.1084/jem.159.3.679
Klinakis, A. et al. A novel tumour-suppressor function for the Notch pathway in myeloid leukaemia. Nature 473, 230–233 (2011).
doi: 10.1038/nature09999
Song, R. et al. Mind bomb 1 in the lymphopoietic niches is essential for T and marginal zone B cell development. J. Exp. Med. 205, 2525–2536 (2008).
doi: 10.1084/jem.20081344
Poulos, M. G. et al. Endothelial Jagged-1 is necessary for homeostatic and regenerative hematopoiesis. Cell Reports 4, 1022–1034 (2013).
doi: 10.1016/j.celrep.2013.07.048
Koch, U. et al. Delta-like 4 is the essential, nonredundant ligand for Notch1 during thymic T cell lineage commitment. J. Exp. Med. 205, 2515–2523 (2008).
doi: 10.1084/jem.20080829
Schmitt, T. M., Ciofani, M., Petrie, H. T. & Zúñiga-Pflücker, J. C. Maintenance of T cell specification and differentiation requires recurrent Notch receptor–ligand interactions. J. Exp. Med. 200, 469–479 (2004).
doi: 10.1084/jem.20040394
Lehar, S. M., Dooley, J., Farr, A. G. & Bevan, M. J. Notch ligands Delta1 and Jagged1 transmit distinct signals to T-cell precursors. Blood 105, 1440–1447 (2005).
doi: 10.1182/blood-2004-08-3257
Olsson, A. et al. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature 537, 698–702 (2016).
doi: 10.1038/nature19348
Paul, F. et al. Transcriptional heterogeneity and lineage commitment in myeloid progenitors. Cell 163, 1663–1677 (2015).
doi: 10.1016/j.cell.2015.11.013
Pronk, C. J. et al. Elucidation of the phenotypic, functional, and molecular topography of a myeloerythroid progenitor cell hierarchy. Cell Stem Cell 1, 428–442 (2007).
doi: 10.1016/j.stem.2007.07.005
Ng, S. Y., Yoshida, T., Zhang, J. & Georgopoulos, K. Genome-wide lineage-specific transcriptional networks underscore Ikaros-dependent lymphoid priming in hematopoietic stem cells. Immunity 30, 493–507 (2009).
doi: 10.1016/j.immuni.2009.01.014
Acar, M. et al. Deep imaging of bone marrow shows non-dividing stem cells are mainly perisinusoidal. Nature 526, 126–130 (2015).
doi: 10.1038/nature15250
Pietras, E. M. et al. Functionally distinct subsets of lineage-biased multipotent progenitors control blood production in normal and regenerative conditions. Cell Stem Cell 17, 35–46 (2015).
doi: 10.1016/j.stem.2015.05.003
Giladi, A. et al. Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis. Nat. Cell Biol. 20, 836–846 (2018).
doi: 10.1038/s41556-018-0121-4
Jacobsen, S. E. W. & Nerlov, C. Haematopoiesis in the era of advanced single-cell technologies. Nat. Cell Biol. 21, 2–8 (2019).
doi: 10.1038/s41556-018-0227-8
Passaro, D. et al. CXCR4 is required for leukemia-initiating cell activity in T cell acute lymphoblastic leukemia. Cancer Cell 27, 769–779 (2015).
doi: 10.1016/j.ccell.2015.05.003
Pitt, L. A. et al. CXCL12-producing vascular endothelial niches control acute T cell leukemia maintenance. Cancer Cell 27, 755–768 (2015).
doi: 10.1016/j.ccell.2015.05.002
Alva, J. A. et al. VE-Cadherin-Cre-recombinase transgenic mouse: a tool for lineage analysis and gene deletion in endothelial cells. Dev. Dyn. 235, 759–767 (2006).
doi: 10.1002/dvdy.20643
DeFalco, J. et al. Virus-assisted mapping of neural inputs to a feeding center in the hypothalamus. Science 291, 2608–2613 (2001).
doi: 10.1126/science.1056602
Kim, J. E., Nakashima, K. & de Crombrugghe, B. Transgenic mice expressing a ligand-inducible Cre recombinase in osteoblasts and odontoblasts: a new tool to examine physiology and disease of postnatal bone and tooth. Am. J. Pathol. 165, 1875–1882 (2004).
doi: 10.1016/S0002-9440(10)63240-3
Madisen, L. et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 13, 133–140 (2010).
doi: 10.1038/nn.2467
Economides, A. N. et al. Conditionals by inversion provide a universal method for the generation of conditional alleles. Proc. Natl Acad. Sci. USA 110, E3179–E3188 (2013).
doi: 10.1073/pnas.1217812110
Hozumi, K. et al. Delta-like 1 is necessary for the generation of marginal zone B cells but not T cells in vivo. Nat. Immunol. 5, 638–644 (2004).
doi: 10.1038/ni1075
Lee, E. C. et al. A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73, 56–65 (2001).
doi: 10.1006/geno.2000.6451
Reizis, B. & Leder, P. The upstream enhancer is necessary and sufficient for the expression of the pre-T cell receptor α gene in immature T lymphocytes. J. Exp. Med. 194, 979–990 (2001).
doi: 10.1084/jem.194.7.979
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
doi: 10.1093/bioinformatics/bts635
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
doi: 10.1093/bioinformatics/btt656
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
doi: 10.1186/s13059-014-0550-8
Zheng, G. X. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).
doi: 10.1038/ncomms14049
Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).
doi: 10.1016/j.cell.2015.05.002
Mayer, C. et al. Developmental diversification of cortical inhibitory interneurons. Nature 555, 457–462 (2018).
doi: 10.1038/nature25999
Rodda, L. B. et al. Single-cell RNA sequencing of lymph node stromal cells reveals niche-associated heterogeneity. Immunity 48, 1014–1028.e6 (2018).
doi: 10.1016/j.immuni.2018.04.006
Finak, G. et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 278 (2015).
doi: 10.1186/s13059-015-0844-5
Tirosh, I. et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352, 189–196 (2016).
doi: 10.1126/science.aad0501
Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381–386 (2014).
doi: 10.1038/nbt.2859
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012).
doi: 10.1089/omi.2011.0118
Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).
doi: 10.1186/1471-2105-14-128