1. Cell Biology
  2. Computational and Systems Biology

Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury

  1. Nona Farbehi
  2. Ralph Patrick
  3. Aude Dorison
  4. Munira Xaymardan
  5. Vaibhao Janbandhu
  6. Katharina Wystub-Lis
  7. Joshua W K Ho
  8. Robert E Nordon  Is a corresponding author
  9. Richard P Harvey  Is a corresponding author
  1. Victor Chang Cardiac Research Institute, Australia
  2. University of New South Wales, Australia
https://doi.org/10.7554/eLife.43882
Share this article
Cite this article
  1. Nona Farbehi
  2. Ralph Patrick
  3. Aude Dorison
  4. Munira Xaymardan
  5. Vaibhao Janbandhu
  6. Katharina Wystub-Lis
  7. Joshua W K Ho
  8. Robert E Nordon
  9. Richard P Harvey
(2019)
Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury
eLife 8:e43882.
https://doi.org/10.7554/eLife.43882
  2. Download BibTeX
  3. Download .RIS

Abstract

Besides cardiomyocytes (CM), the heart contains numerous stromal cell types which play key roles in heart repair, regeneration and disease, including fibroblast, vascular and immune cells. However, a comprehensive understanding of this interactive cell community is lacking. We performed single cell RNA-sequencing of the total non-CM fraction and enriched (Pdgfra-GFP+) fibroblast lineage cells from murine hearts at days 3 and 7 post-sham or myocardial infarction surgery. Clustering of >30,000 single cells allowed us to identify >30 populations representing 9 cell lineages, included a previously undescribed fibroblast lineage trajectory present in both sham and MI hearts leading to a uniquely activated cell state defined in part by a strong anti-WNT transcriptome signature. We also defined three novel myofibroblast subtypes expressing either pro-fibrotic or anti-fibrotic signatures, and 8 macrophage subsets. These comprehensive cardiac single cell transcriptome data provide an entry point for deeper analysis of cardiac homeostasis, inflammation, fibrosis, repair and regeneration.

Data availability

Sequencing data have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession codes E-MTAB-7376 and E-MTAB-7365.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Nona Farbehi

    Developmental and Stem Cell Biology, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
    Competing interests
    No competing interests declared.

  2. Ralph Patrick

    Developmental and Stem Cell Biology, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0956-1026

  3. Aude Dorison

    Developmental and Stem Cell Biology, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
    Competing interests
    No competing interests declared.

  4. Munira Xaymardan

    Developmental and Stem Cell Biology, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
    Competing interests
    No competing interests declared.

  5. Vaibhao Janbandhu

    Developmental and Stem Cell Biology, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
    Competing interests
    No competing interests declared.

  6. Katharina Wystub-Lis

    Developmental and Stem Cell Biology, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
    Competing interests
    No competing interests declared.

  7. Joshua W K Ho

    Developmental and Stem Cell Biology, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
    Competing interests
    No competing interests declared.

  8. Robert E Nordon

    Graduate School of Biomedical Engineering, University of New South Wales, Kensington, Australia
    For correspondence
    r.nordon@unsw.edu.au
    Competing interests
    No competing interests declared.

  9. Richard P Harvey

    Developmental and Stem Cell Biology, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
    For correspondence
    r.harvey@victorchang.edu.au
    Competing interests
    Richard P Harvey, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9950-9792

Funding

Stem Cells Australia (SR110001002)

  • Richard P Harvey

National Health and Medical Research Council (1118576)

  • Richard P Harvey

National Health and Medical Research Council (1074386)

  • Richard P Harvey

Fondation Leducq (15CVD03)

  • Richard P Harvey

National Heart Foundation of Australia (100848)

  • Joshua W K Ho

St. Vincent's Clinic Foundation and New South Wales Government Cardiovascular Research Network (100711)

  • Richard P Harvey

University of New South Wales

  • Nona Farbehi

Fondation Leducq (13CVD01)

  • Richard P Harvey

National Health and Medical Research Council (1105271)

  • Joshua W K Ho

National Health and Medical Research Council (573707)

  • Richard P Harvey

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

Ethics

Animal experimentation: This research was performed following the guidelines, and with the approval, of the Garvan Institute of Medical Research/St. Vincent's Animal Experimentation Ethics Committee (research approvals 13/01, 13/02, 16/03 and 16/10).

Copyright

© 2019, Farbehi 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

  • 25,769
    views
  • 3,438
    downloads
  • 411
    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. Nona Farbehi
  2. Ralph Patrick
  3. Aude Dorison
  4. Munira Xaymardan
  5. Vaibhao Janbandhu
  6. Katharina Wystub-Lis
  7. Joshua W K Ho
  8. Robert E Nordon
  9. Richard P Harvey
(2019)
Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury
eLife 8:e43882.
https://doi.org/10.7554/eLife.43882

Share this article

https://doi.org/10.7554/eLife.43882

Categories and tags

Research organism

Further reading

    1. Cell Biology

    Oversized cells activate global proteasome-mediated protein degradation to maintain cell size homeostasis

    Shixuan Liu, Ceryl Tan ... Ran Kafri
    Research Advance

    Proliferating animal cells maintain a stable size distribution over generations despite fluctuations in cell growth and division size. Previously, we showed that cell size control involves both cell size checkpoints, which delay cell cycle progression in small cells, and size-dependent regulation of mass accumulation rates (Ginzberg et al., 2018). While we previously identified the p38 MAPK pathway as a key regulator of the mammalian cell size checkpoint (S. Liu et al., 2018), the mechanism of size-dependent growth rate regulation has remained elusive. Here, we quantified global rates of protein synthesis and degradation in cells of varying sizes, both under unperturbed conditions and in response to perturbations that trigger size-dependent compensatory growth slowdown. We found that protein synthesis rates scale proportionally with cell size across cell cycle stages and experimental conditions. In contrast, oversized cells that undergo compensatory growth slowdown exhibit a superlinear increase in proteasome-mediated protein degradation, with accelerated protein turnover per unit mass, suggesting activation of the proteasomal degradation pathway. Both nascent and long-lived proteins contribute to the elevated protein degradation during compensatory growth slowdown, with long-lived proteins playing a crucial role at the G1/S transition. Notably, large G1/S cells exhibit particularly high efficiency in protein degradation, surpassing that of similarly sized or larger cells in S and G2, coinciding with the timing of the most stringent size control in animal cells. These results collectively suggest that oversized cells reduce their growth efficiency by activating global proteasome-mediated protein degradation to promote cell size homeostasis.

    1. Cell Biology
    2. Physics of Living Systems

    A high-throughput platform for single-molecule tracking identifies drug interaction and cellular mechanisms

    David Trombley McSwiggen, Helen Liu ... Hilary P Beck
    Research Article

    The regulation of cell physiology depends largely upon interactions of functionally distinct proteins and cellular components. These interactions may be transient or long-lived, but often affect protein motion. Measurement of protein dynamics within a cellular environment, particularly while perturbing protein function with small molecules, may enable dissection of key interactions and facilitate drug discovery; however, current approaches are limited by throughput with respect to data acquisition and analysis. As a result, studies using super-resolution imaging are typically drawing conclusions from tens of cells and a few experimental conditions tested. We addressed these limitations by developing a high-throughput single-molecule tracking (htSMT) platform for pharmacologic dissection of protein dynamics in living cells at an unprecedented scale (capable of imaging >106 cells/day and screening >104 compounds). We applied htSMT to measure the cellular dynamics of fluorescently tagged estrogen receptor (ER) and screened a diverse library to identify small molecules that perturbed ER function in real time. With this one experimental modality, we determined the potency, pathway selectivity, target engagement, and mechanism of action for identified hits. Kinetic htSMT experiments were capable of distinguishing between on-target and on-pathway modulators of ER signaling. Integrated pathway analysis recapitulated the network of known ER interaction partners and suggested potentially novel, kinase-mediated regulatory mechanisms. The sensitivity of htSMT revealed a new correlation between ER dynamics and the ability of ER antagonists to suppress cancer cell growth. Therefore, measuring protein motion at scale is a powerful method to investigate dynamic interactions among proteins and may facilitate the identification and characterization of novel therapeutics.

    1. Cell Biology
    2. Neuroscience

    Psychological stress disturbs bone metabolism via miR-335-3p/Fos signaling in osteoclast

    Jiayao Zhang, Juan Li ... Weicai Liu
    Research Article

    It has been well validated that chronic psychological stress leads to bone loss, but the underlying mechanism remains unclarified. In this study, we established and analyzed the chronic unpredictable mild stress (CUMS) mice to investigate the miRNA-related pathogenic mechanism involved in psychological stress-induced osteoporosis. Our result found that these CUMS mice exhibited osteoporosis phenotype that is mainly attributed to the abnormal activities of osteoclasts. Subsequently, miRNA sequencing and other analysis showed that miR-335-3p, which is normally highly expressed in the brain, was significantly downregulated in the nucleus ambiguous, serum, and bone of the CUMS mice. Additionally, in vitro studies detected that miR-335-3p is important for osteoclast differentiation, with its direct targeting site in Fos. Further studies demonstrated FOS was upregulated in CUMS osteoclast, and the inhibition of FOS suppressed the accelerated osteoclastic differentiation, as well as the expression of osteoclastic genes, such as Nfatc1, Acp5, and Mmp9, in miR-335-3p-restrained osteoclasts. In conclusion, this work indicated that psychological stress may downregulate the miR-335-3p expression, which resulted in the accumulation of FOS and the upregulation of NFACT1 signaling pathway in osteoclasts, leading to its accelerated differentiation and abnormal activity. These results decipher a previously unrecognized paradigm that miRNA can act as a link between psychological stress and bone metabolism.