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Cellular plasticity of the bone marrow niche promotes hematopoietic stem cell regeneration

Abstract

Hematopoietic stem cells (HSCs) regenerate after myeloablation, a procedure that adversely disrupts the bone marrow and drives leptin receptor-expressing cells, a key niche component, to differentiate extensively into adipocytes. Regeneration of the bone marrow niche is associated with the resolution of adipocytes, but the mechanisms remain poorly understood. Using Plin1-creER knock-in mice, we followed the fate of adipocytes in the regenerating niche in vivo. We found that bone marrow adipocytes were highly dynamic and dedifferentiated to leptin receptor-expressing cells during regeneration after myeloablation. Bone marrow adipocytes could give rise to osteolineage cells after skeletal injury. The cellular fate of steady-state bone marrow adipocytes was also plastic. Deletion of adipose triglyceride lipase (Atgl) from bone marrow stromal cells, including adipocytes, obstructed adipocyte dedifferentiation and led to severely compromised regeneration of HSCs as well as impaired B lymphopoiesis after myeloablation, but not in the steady state. Thus, the regeneration of HSCs and their niche depends on the cellular plasticity of bone marrow adipocytes.

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Fig. 1: Expanded adipocytes contract in parallel with bone marrow regeneration after irradiation.
Fig. 2: Bone marrow adipocytes dedifferentiate to mesenchymal stromal cells during bone marrow regeneration after irradiation.
Fig. 3: snRNA-seq reveals mesenchymal stromal cell populations in the regenerating bone marrow.
Fig. 4: Adipocyte-derived mesenchymal stromal cells contribute to osteolineage cells.
Fig. 5: Bone marrow adipocytes can dedifferentiate to stromal cells and bone marrow adipocyte-derived cells can differentiate into osteolineage cells without myeloablation.
Fig. 6: Prx1-cre; Atglfl/fl mice exhibit normal hematopoiesis in the steady state.
Fig. 7: Conditional deletion of Atgl impedes adipocyte dedifferentiation and leads to HSC depletion from the bone marrow after irradiation.

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Data availability

The snRNA-seq data generated by this study have been deposited in the NCBI Gene Expression Omnibus (GEO) repository under accession number GSE227255. Source data are provided with this paper.

Code availability

Standard bioinformatics pipelines used for analyzing snRNA-seq data were described in the ‘snRNA-seq’ section. All codes that have been used in the study are available at https://doi.org/10.5281/zenodo.8280830 (ref. 52) and https://github.com/LeiDingLab/Nature_Genetics_2023.

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Acknowledgements

This work was supported by the Rita Allen Foundation, the Schaefer Scholar program, and the National Heart, Lung and Blood Institute (grant nos. R01HL132074 and R01HL153487). L.D. was also supported by a Scholar Award from the Leukemia and Lymphoma Society, grant no. R01HL155868, and grant no. R01GM146061 from the National Institutes of Health (NIH). H.H. was supported by the Uehara Memorial Foundation and the Japan Society for the Promotion of Science. L.G. was supported by a NYSTEM training grant and an American Heart Association postdoctoral fellowship. We thank M. Kissner and R. Gordon-Schneider at the Columbia Stem Cell Initiative for help on flow cytometry. We thank E. DiMaulo-Milk for critically reading the manuscript. This research was funded in part through the NIH/National Cancer Institute Cancer Center Support Grant, grant nos. P30CA013696 and P41EB027062.

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Authors and Affiliations

Authors

Contributions

H.H. performed all of the experiments. L.G. performed analysis on the snRNA-seq data. D.N.T. and G.V.-N. helped with the adipocyte culture experiments and editing of the manuscript. H.H. and L.D. designed the experiments, interpreted the results and wrote the manuscript.

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Correspondence to Lei Ding.

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Extended data

Extended Data Fig. 1 Bone marrow regenerates after irradiation.

a-j, Kinetics of maturing bone marrow hematopoietic cells after sublethal irradiation (6 Gy). Irradiated wild-type mice were analyzed at 2 weeks (2 w), 5 weeks (5 w), and 8 weeks (8 w) post-irradiation. Non-irradiated mice were used as controls (Con). The frequencies and numbers of CD3+ cells (a, b), B220+ cells (c, d), Gr1+ Mac1+ cells (e, f), Ter119+ cells (g, h), and CD41+ cells (i, j) are shown (n = 4 for each group). All data represent mean ± SD. One-way ANOVAs followed by Dunnett’s test were used to assess statistical significance.

Source data

Extended Data Fig. 2 The generation of a Plin1creER knockin allele.

a, Clustering of bone marrow cells based on t-Distributed Stochastic Neighbor Embedding (t-SNE) from published data12. b, Gene expression levels of Lepr, Adipoq, and Plin1 overlaid on t-SNE visualization. c, Clustering of bone marrow cells based on t-SNE from published data11. d, Gene expression levels of Lepr, Adipoq, and Plin1 overlaid on t-SNE visualization. e, RT-PCR analyses revealed that Plin1 is expressed by adipose tissues but not bone marrow mesenchymal stromal cells. Adipoq is expressed by bone marrow mesenchymal stromal cells while Ucp1 is only expressed by brown adipose tissue. β-Actin was used as a control for RT-PCR. Lane 1: Brown Adipose Tissue (BAT), Lane 2: White Adipose Tissue (WAT), Lane 3: sorted CD45/Ter119/CD31PDGFRα+ bone marrow mesenchymal stromal cells (n = 1). f, Gene targeting strategy. Plin1creER was generated by inserting P2A-creER into the ninth exon of Plin1 using homologous recombination in ES cells. g, Representative genotyping PCR results confirmed the germline transmission of the Plin1creER allele (Lane 1: creER/creER, Lane 2: creER/+, Lane 3: +/+) (n = 3). h, Representative image of the bone marrow from creER/creER homozygous mice (n = 2). Adipocytes were stained with an anti-perilipin antibody (in green). Nuclei were stained with DAPI (in blue). The square indicates an enlarged region. Scale bar, 100 μm. i-k, Sublethally irradiated (6 Gy) wild-type mice were treated with three doses of corn oil or tamoxifen on days 10, 12, and 14 and analyzed on day 15 post-irradiation. Experimental scheme (i). Representative images of the bone marrow (j). Quantification of bone marrow adipocytes stained with an anti-perilipin antibody (n = 3 for each group) (k). Scale bars, 50 μm. l, Representative whole-mount confocal images and frequency of perilipin+ adipocytes that were tdTomato+ (n = 3) in the bone marrow from Plin1creER; Rosa26LSL-tdTomato mice treated with tamoxifen on days 10, 12, and 14 and analyzed on day 15 post-irradiation. Scale bar, 100 μm. m, Individual channels of Fig. 2c (15 d). Scale bar, 100 μm. All data represent mean ± SD. A two-sided Student’s t-test was used to assess statistical significance in k.

Source data

Extended Data Fig. 3 Prominent dedifferentiation of bone marrow adipocyte was evident with Plin1-creER induction by a low dose of tamoxifen.

a, Experimental scheme. b, c, Irradiated Plin1creER; Rosa26LSL-tdTomato mice were administered 0.2 mg tamoxifen on day 14 post-irradiation and analyzed 36 hours (36 hr) later (n = 3). Representative images of the bone marrow are shown. Scale bar, 50 μm. d, A representative flow cytometric plot showing no labeling of stromal cells in enzymatically digested bone marrow from irradiated Plin1creER; Rosa26LSL-tdTomato mice treated with 0.2 mg tamoxifen on day 14 post-irradiation and analyzed 36 hours (36 hr) later (n = 3). e, f, Irradiated Plin1creER; Rosa26LSL-tdTomato mice were administered 0.2 mg tamoxifen on day 14 and analyzed 6 weeks (6 w) later (n = 5). Representative images of the bone marrow are shown. Scale bar, 50 μm. g, A representative flow cytometric plot of enzymatically digested bone marrow cells of the tibia from irradiated Plin1creER; Rosa26LSL-tdTomato mice treated as in e and f (n = 6). h, Frequency of tdTomato+ cells that were perilipin in the bone marrow of irradiated Plin1creER; Rosa26LSL-tdTomato mice treated with 0.2 mg tamoxifen on day 14 post-irradiation and analyzed 6 weeks later (n = 5). i, Representative image showing adipocyte-derived tdTomato+ bone marrow stromal cells from irradiated Plin1creER; Rosa26LSL-tdTomato mice expressed LepR (arrows) (n = 2). The mice were treated with 0.2 mg tamoxifen on day 14 after irradiation and analyzed 6 weeks later. Scale bar, 50 μm. All data represent mean ± SD.

Source data

Extended Data Fig. 4 Dedifferentiation of bone marrow adipocytes following 5FU challenge.

a, Representative images of the bone marrow showing adipocyte content from the nontreated control (Con), 10 days (10 d), 4 weeks (4 w), or 6 weeks (6 w) after 5FU (150 mg kg-1) administration in wild-type mice. Adipocytes were stained with an anti-perilipin antibody (in green). Scale bars, 100 μm. b, Quantification of bone marrow adipocytes following 5FU treatment (n = 3 for each group). c-e, Plin1creER; Rosa26LSL-tdTomato mice were treated with 3 doses of tamoxifen on days 6, 8, and 10 and analyzed 4 weeks (4 w) and 6 weeks (6 w) after 5FU treatment. Representative images of the bone marrow (c), the frequency of adipocytes that were tdTomato+ (n = 3 for each group) (d), and the frequency of tdTomato+ cells that were perilipin- (n = 3 for each group) (e) are shown. Scale bars, 100 μm. f, Representative image showing that adipocyte-derived stromal cells express LepR (arrows) in the bone marrow from Plin1creER; Rosa26LSL-tdTomato mice after 5FU treatment (n = 3). The mice were treated with tamoxifen on days 6, 8, and 10, and analyzed 4 weeks after 5FU treatment. The square indicates an enlarged region. Scale bar, 50 μm. All data represent mean ± SD. A one-way ANOVA followed by Dunnett’s test was used in b. Two-sided Student’s t-tests were used in d and e.

Source data

Extended Data Fig. 5 snRNA-seq reveals stromal contribution by bone marrow adipocytes during regeneration.

a, Heatmap showing the signature genes of two distinct mesenchymal cell clusters in the regenerating bone marrow (Lepr+ and Adipocyte). The Lepr+ cluster is further divided into two clusters (Lepr+_Osteo and Lepr+_Adipo). b, Violin plots showing the expression levels of Lepr, Adipoq, and Alpl. c, d, Expression levels of Perilipin family genes (Plin1, Plin2, Plin3, Plin4, and Plin5) and three genes coding lipases (Atgl, Lipe, and Mgll) are shown in violin plots (c) and dot plot (d). e, Dot plot showing the expression levels of Adrb1, Adrb2, Adrb3, and Il6ra.

Extended Data Fig. 6 Ex vivo properties of mature bone marrow adipocytes and their derivatives.

a, Experimental scheme for monitoring bone marrow adipocyte culture in vitro. Individual bone marrow adipocytes isolated from Plin1creER; Rosa26LSL-tdTomato mice at 15 days after sublethal irradiation (tamoxifen administration on day 14) were followed by time-lapse imaging in culture for 7 days. Lipid-filled adipocytes adhering to the ceiling of the flask on day 2 were tracked by confocal microscopy. b, Representative images of live cell imaging of bone marrow tdTomato+ adipocytes and their derivatives from day 2 to 7 (n = 2). Arrows point to adipocyte-derived cells (tdTomato+) with a stromal morphology but lacking lipid droplets (LipiDye II negative). Lipid droplets were stained with LipiDye II (in green). Scale bars, 50 μm. c, Experimental scheme for testing stromal cell function in vitro. d, Sublethally irradiated Plin1creER; Rosa26LSL-tdTomato mice were administered tamoxifen on days 10, 12, and 14 post-irradiation. At 8 weeks post-irradiation, CFU-F assays were performed with enzymatically digested bone marrow cells. Attached cells at clonal density were counted one day after plating and colonies were counted 12 days later. A representative image of a CFU-F colony (>25 cells) stained by Crystal Violet is shown. Scale bar, 500 μm. e, A representative image showing that tdTomato+ stromal cells are proliferative. The cells were from single tdTomato+ cells. Scale bar, 200 μm. f, Quantifications of CFU-F frequency from attached tdTomato and tdTomato+ stromal cells (n = 4). g, Representative images of live cell imaging of a single tdTomato+ cell for 5 days. Lipid droplets were stained by LipiDye II (in green, arrow) on day 5 to show that lipid droplets are accumulating in a tdTomato+ cell. Scale bars, 50 μm. h, Quantification of adipocyte frequency from attached tdTomato and tdTomato+ stromal cells (n = 4). After initiation of cell culture as in c, cells were cultured in a normal media without differentiation induction for 12 days and then LipiDye II+ adipocytes were counted. i, A representative image of a colony stained by Alizarin Red S showing osteoblastic differentiation. Scale bar, 500 μm. j, Quantification of CFU-osteoblasts (CFU-Ob) frequency from attached tdTomato- and tdTomato+ stromal cells (n = 4). After initiation of cell culture as in c, cells were cultured in a normal media for 12 days and then cultured in osteolineage differentiation media for 14 days. All data represent mean ± SD. Two-sided Student’s t-tests were used to assess statistical significance.

Source data

Extended Data Fig. 7 Perturbed lymphopoiesis in the bone marrow of Prx1-cre; Atglfl/fl mice after irradiation.

a-e, The frequencies and numbers of CD3+ cells (a), B220+ cells (b), Gr1+ Mac1+ cells (c), Ter119+ cells (d) and CD41+ cells (e) in the bone marrow of Prx1-cre; Atglfl/fl (Mut) and control mice (Con) (n = 7 for Con, n = 6 for Mut). f-i, Representative flow cytometric plots of LK (Lin c-Kit+) cells from Prx1cre; Atglfl/fl (Mut) and control mice (Con) at 8 weeks post-irradiation (f). Quantifications of CMP number (g), GMP number (h), and MEP number (i) in the bone marrow of Mut and Con at 15 days (n = 4 for each group) and 8 weeks (n = 6 for each group) post-irradiation. j, The number of CD45/Ter119/CD31PDGFRα+ bone marrow mesenchymal stromal cells of Prx1cre; Atglfl/fl (Mut) and control mice (Con) at 8 weeks post-irradiation (n = 5 for each group). A one-sided Student’s t-test was used. k-o, Representative flow cytometric plots and frequencies of bone marrow cells that are positive for CD3 (k), B220 (l), Gr1 and Mac1 (m), Ter119 (n), and CD41 (o). Prx1-cre; Atglfl/fl (Mut) and control mice (Con) were analyzed at 8 weeks post-irradiation (n = 8 for Con, n = 9 for Mut). p, Experimental scheme for transplantation assays in Fig. 7m. Competitive transplantation of 106 bone marrow cells (CD45.2) from Prx1-cre; Atglfl/f or control mice with 106 competitor bone marrow cells (CD45.1) into lethally irradiated recipients. Donor and competitor cells were harvested from sublethally irradiated mice at 8 weeks post-irradiation. All data represent mean ± SD. Two-sided Student’s t-tests were used in a-e, g-i, and k-o.

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Hirakawa, H., Gao, L., Tavakol, D.N. et al. Cellular plasticity of the bone marrow niche promotes hematopoietic stem cell regeneration. Nat Genet 55, 1941–1952 (2023). https://doi.org/10.1038/s41588-023-01528-2

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