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The bone marrow microenvironment at single-cell resolution

Author

Listed:
  • Anastasia N. Tikhonova

    (NYU School of Medicine
    NYU School of Medicine)

  • Igor Dolgalev

    (NYU School of Medicine
    NYU School of Medicine
    NYU School of Medicine)

  • Hai Hu

    (NYU School of Medicine
    NYU School of Medicine)

  • Kishor K. Sivaraj

    (Faculty of Medicine)

  • Edlira Hoxha

    (NYU School of Medicine
    NYU School of Medicine)

  • Álvaro Cuesta-Domínguez

    (Columbia University)

  • Sandra Pinho

    (Albert Einstein College of Medicine)

  • Ilseyar Akhmetzyanova

    (Albert Einstein College of Medicine)

  • Jie Gao

    (Regeneron Genetics Center)

  • Matthew Witkowski

    (NYU School of Medicine
    NYU School of Medicine)

  • Maria Guillamot

    (NYU School of Medicine
    NYU School of Medicine)

  • Michael C. Gutkin

    (Hackensack University Medical Center)

  • Yutong Zhang

    (Division of Advanced Research Technologies, NYU School of Medicine)

  • Christian Marier

    (Division of Advanced Research Technologies, NYU School of Medicine)

  • Catherine Diefenbach

    (NYU School of Medicine
    NYU School of Medicine)

  • Stavroula Kousteni

    (Columbia University)

  • Adriana Heguy

    (NYU School of Medicine
    NYU School of Medicine
    Division of Advanced Research Technologies, NYU School of Medicine)

  • Hua Zhong

    (NYU School of Medicine)

  • David R. Fooksman

    (Albert Einstein College of Medicine)

  • Jason M. Butler

    (Hackensack University Medical Center)

  • Aris Economides

    (Regeneron Genetics Center)

  • Paul S. Frenette

    (Albert Einstein College of Medicine)

  • Ralf H. Adams

    (Faculty of Medicine)

  • Rahul Satija

    (New York Genome Center)

  • Aristotelis Tsirigos

    (NYU School of Medicine
    NYU School of Medicine
    NYU School of Medicine)

  • Iannis Aifantis

    (NYU School of Medicine
    NYU School of Medicine)

Abstract

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.

Suggested Citation

  • Anastasia N. Tikhonova & Igor Dolgalev & Hai Hu & Kishor K. Sivaraj & Edlira Hoxha & Álvaro Cuesta-Domínguez & Sandra Pinho & Ilseyar Akhmetzyanova & Jie Gao & Matthew Witkowski & Maria Guillamot & Mi, 2019. "The bone marrow microenvironment at single-cell resolution," Nature, Nature, vol. 569(7755), pages 222-228, May.
  • Handle: RePEc:nat:nature:v:569:y:2019:i:7755:d:10.1038_s41586-019-1104-8
    DOI: 10.1038/s41586-019-1104-8
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    Cited by:

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    2. Yinghui Li & Mei He & Wenshan Zhang & Wei Liu & Hui Xu & Ming Yang & Hexiao Zhang & Haiwei Liang & Wenjing Li & Zhaozhao Wu & Weichao Fu & Shiqi Xu & Xiaolei Liu & Sibin Fan & Liwei Zhou & Chaoqun Wan, 2023. "Expansion of human megakaryocyte-biased hematopoietic stem cells by biomimetic Microniche," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Jialiang S. Wang & Tushar Kamath & Courtney M. Mazur & Fatemeh Mirzamohammadi & Daniel Rotter & Hironori Hojo & Christian D. Castro & Nicha Tokavanich & Rushi Patel & Nicolas Govea & Tetsuya Enishi & , 2021. "Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin," Nature Communications, Nature, vol. 12(1), pages 1-20, December.
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    6. Xianzhu Zhang & Wei Jiang & Chang Xie & Xinyu Wu & Qian Ren & Fei Wang & Xilin Shen & Yi Hong & Hongwei Wu & Youguo Liao & Yi Zhang & Renjie Liang & Wei Sun & Yuqing Gu & Tao Zhang & Yishan Chen & Wei, 2022. "Msx1+ stem cells recruited by bioactive tissue engineering graft for bone regeneration," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    7. Alicia Villatoro & Vincent Cuminetti & Aurora Bernal & Carlos Torroja & Itziar Cossío & Alberto Benguría & Marc Ferré & Joanna Konieczny & Enrique Vázquez & Andrea Rubio & Peter Utnes & Almudena Tello, 2023. "Endogenous IL-1 receptor antagonist restricts healthy and malignant myeloproliferation," Nature Communications, Nature, vol. 14(1), pages 1-28, December.
    8. Young-Woong Kim & Greta Zara & HyunJun Kang & Sergio Branciamore & Denis O’Meally & Yuxin Feng & Chia-Yi Kuan & Yingjun Luo & Michael S. Nelson & Alex B. Brummer & Russell Rockne & Zhen Bouman Chen & , 2022. "Integration of single-cell transcriptomes and biological function reveals distinct behavioral patterns in bone marrow endothelium," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    9. Joschka Heil & Victor Olsavszky & Katrin Busch & Kay Klapproth & Carolina Torre & Carsten Sticht & Kajetan Sandorski & Johannes Hoffmann & Hiltrud Schönhaber & Johanna Zierow & Manuel Winkler & Christ, 2021. "Bone marrow sinusoidal endothelium controls terminal erythroid differentiation and reticulocyte maturation," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    10. Runfeng Miao & Harim Chun & Xing Feng & Ana Cordeiro Gomes & Jungmin Choi & João P. Pereira, 2022. "Competition between hematopoietic stem and progenitor cells controls hematopoietic stem cell compartment size," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    11. Natthakan Thongon & Feiyang Ma & Andrea Santoni & Matteo Marchesini & Elena Fiorini & Ashley Rose & Vera Adema & Irene Ganan-Gomez & Emma M. Groarke & Fernanda Gutierrez-Rodrigues & Shuaitong Chen & P, 2021. "Hematopoiesis under telomere attrition at the single-cell resolution," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    12. Christina M. Termini & Amara Pang & Tiancheng Fang & Martina Roos & Vivian Y. Chang & Yurun Zhang & Nicollette J. Setiawan & Lia Signaevskaia & Michelle Li & Mindy M. Kim & Orel Tabibi & Paulina K. Li, 2021. "Neuropilin 1 regulates bone marrow vascular regeneration and hematopoietic reconstitution," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    13. Yoshiki Omatsu & Shota Aiba & Tomonori Maeta & Kei Higaki & Kazunari Aoki & Hitomi Watanabe & Gen Kondoh & Riko Nishimura & Shu Takeda & Ung-il Chung & Takashi Nagasawa, 2022. "Runx1 and Runx2 inhibit fibrotic conversion of cellular niches for hematopoietic stem cells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    14. Raymond K. H. Yip & Joel S. Rimes & Bianca D. Capaldo & François Vaillant & Kellie A. Mouchemore & Bhupinder Pal & Yunshun Chen & Elliot Surgenor & Andrew J. Murphy & Robin L. Anderson & Gordon K. Smy, 2021. "Mammary tumour cells remodel the bone marrow vascular microenvironment to support metastasis," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    15. Adrienne Anginot & Julie Nguyen & Zeina Abou Nader & Vincent Rondeau & Amélie Bonaud & Maria Kalogeraki & Antoine Boutin & Julia P. Lemos & Valeria Bisio & Joyce Koenen & Lea Hanna Doumit Sakr & Amand, 2023. "WHIM Syndrome-linked CXCR4 mutations drive osteoporosis," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    16. Marco Angelozzi & Anirudha Karvande & Véronique Lefebvre, 2024. "SOXC are critical regulators of adult bone mass," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    17. Yang Liu & Qi Chen & Hyun-Woo Jeong & Bong Ihn Koh & Emma C. Watson & Cong Xu & Martin Stehling & Bin Zhou & Ralf H. Adams, 2022. "A specialized bone marrow microenvironment for fetal haematopoiesis," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    18. Robin D. Lee & Sarah A. Munro & Todd P. Knutson & Rebecca S. LaRue & Lynn M. Heltemes-Harris & Michael A. Farrar, 2021. "Single-cell analysis identifies dynamic gene expression networks that govern B cell development and transformation," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    19. Yuki Matsushita & Jialin Liu & Angel Ka Yan Chu & Chiaki Tsutsumi-Arai & Mizuki Nagata & Yuki Arai & Wanida Ono & Kouhei Yamamoto & Thomas L. Saunders & Joshua D. Welch & Noriaki Ono, 2023. "Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis," Nature Communications, Nature, vol. 14(1), pages 1-23, December.

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