Identification of phenotypically, functionally, and anatomically distinct stromal niche populations in human bone marrow based on single-cell RNA sequencing

Abstract

Hematopoiesis is regulated by the bone marrow (BM) stroma. However, cellular identities and functions of the different BM stromal elements in humans remain poorly defined. Based on single-cell RNA sequencing (scRNAseq), we systematically characterized the human non-hematopoietic BM stromal compartment and we investigated stromal cell regulation principles based on the RNA velocity analysis using scVelo and studied the interactions between the human BM stromal cells and hematopoietic cells based on ligand-receptor (LR) expression using CellPhoneDB. scRNAseq led to the identification of six transcriptionally and functionally distinct stromal cell populations. Stromal cell differentiation hierarchy was recapitulated based on RNA velocity analysis and in vitro proliferation capacities and differentiation potentials. Potential key factors that might govern the transition from stem and progenitor cells to fate-committed cells were identified. In situ localization analysis demonstrated that different stromal cells were localized in different niches in the bone marrow. In silico cell-cell communication analysis further predicted that different stromal cell types might regulate hematopoiesis through distinct mechanisms. These findings provide the basis for a comprehensive understanding of the cellular complexity of the human BM microenvironment and the intricate stroma-hematopoiesis crosstalk mechanisms, thus refining our current view on human hematopoietic niche organization.

Data availability

The scRNA-seq matrix data generated in this study have been deposited in the GEO database (GSE190965).

The following data sets were generated

Article and author information

Author details

  1. Hongzhe Li

    Division of Molecular Hematology and Stem Cell Center, Lund University, Lund, Sweden
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7788-878X
  2. Sandro Bräunig

    Division of Molecular Hematology and Stem Cell Center, Lund University, Lund, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  3. Parashar Dhapolar

    Division of Molecular Hematology and Stem Cell Center, Lund University, Lund, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  4. Göran Karlsson

    Division of Molecular Hematology and Stem Cell Center, Lund University, Lund, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  5. Stefan Lang

    Division of Molecular Hematology and Stem Cell Center, Lund University, Lund, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  6. Stefan Scheding

    Division of Molecular Hematology and Stem Cell Center, Lund University, Lund, Sweden
    For correspondence
    stefan.scheding@med.lu.se
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8005-9568

Funding

Swedish Cancer Foundation (20-1163PjF 01H)

  • Stefan Scheding

Swedish Childhood Cancer Foundation (PR2018-0078)

  • Stefan Scheding

Swedish Childhood Cancer Foundation (PR2021-0065)

  • Stefan Scheding

Swedish Bloodcancer Association (N.A.)

  • Stefan Scheding

Swedish Research Council (N.A.)

  • Stefan Scheding

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: Human bone marrow (BM) cells were collected at the Hematology Department, Skåne University Hospital Lund, Sweden, from consenting healthy donors. The use of human samples was approved by the Regional Ethics Review Board in Lund, Sweden.

Copyright

© 2023, Li et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 4,162
    views
  • 681
    downloads
  • 15
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Hongzhe Li
  2. Sandro Bräunig
  3. Parashar Dhapolar
  4. Göran Karlsson
  5. Stefan Lang
  6. Stefan Scheding
(2023)
Identification of phenotypically, functionally, and anatomically distinct stromal niche populations in human bone marrow based on single-cell RNA sequencing
eLife 12:e81656.
https://doi.org/10.7554/eLife.81656

Share this article

https://doi.org/10.7554/eLife.81656

Further reading

    1. Stem Cells and Regenerative Medicine
    Syeda Nayab Fatima Abidi, Sara Chan ... Christian W Siebel
    Research Article

    The sebaceous gland (SG) is a vital appendage of the epidermis, and its normal homeostasis and function is crucial for effective maintenance of the skin barrier. Notch signaling is a well-known regulator of epidermal differentiation, and has also been shown to be involved in postnatal maintenance of SGs. However, the precise role of Notch signaling in regulating SG differentiation in the adult homeostatic skin remains unclear. While there is evidence to suggest that Notch1 is the primary Notch receptor involved in regulating the differentiation process, the ligand remains unknown. Using monoclonal therapeutic antibodies designed to specifically inhibit of each of the Notch ligands or receptors, we have identified the Jag2/Notch1 signaling axis as the primary regulator of sebocyte differentiation in mouse homeostatic skin. Mature sebocytes are lost upon specific inhibition of the Jag2 ligand or Notch1 receptor, resulting in the accumulation of proliferative stem/progenitor cells in the SG. Strikingly, this phenotype is reversible, as these stem/progenitor cells re-enter differentiation when the inhibition of Notch activity is lifted. Thus, Notch activity promotes correct sebocyte differentiation, and is required to restrict progenitor proliferation.

    1. Stem Cells and Regenerative Medicine
    Corentin Bernou, Marc-André Mouthon ... François Dominique Boussin
    Research Article

    The lateral wall of the mouse subventricular zone harbors neural stem cells (NSC, B cells) which generate proliferating transient-amplifying progenitors (TAP, C cells) that ultimately give rise to neuroblasts (NB, A cells). Molecular profiling at the single-cell level struggles to distinguish these different cell types. Here, we combined transcriptome analyses of FACS-sorted cells and single-cell RNAseq to demonstrate the existence of an abundant, clonogenic and multipotent population of immature neuroblasts (iNB cells) at the transition between TAP and migrating NB (mNB). iNB are reversibly engaged in neuronal differentiation. Indeed, they keep molecular features of both undifferentiated progenitors, plasticity and unexpected regenerative properties. Strikingly, they undergo important progressive molecular switches, including changes in the expression of splicing regulators leading to their differentiation in mNB subdividing them into two subtypes, iNB1 and iNB2. Due to their plastic properties, iNB could represent a new target for regenerative therapy of brain damage.