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

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).

Reviewing Editor

  1. Edward Morrisey, University of Pennsylvania, United States

Publication history

  1. Received: November 26, 2018
  2. Accepted: March 25, 2019
  3. Accepted Manuscript published: March 26, 2019 (version 1)
  4. Version of Record published: April 11, 2019 (version 2)

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

  • 19,986
    Page views
  • 2,683
    Downloads
  • 182
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

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

Further reading

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Haikel Dridi et al.
    Research Article Updated

    Age-dependent loss of body wall muscle function and impaired locomotion occur within 2 weeks in Caenorhabditis elegans (C. elegans); however, the underlying mechanism has not been fully elucidated. In humans, age-dependent loss of muscle function occurs at about 80 years of age and has been linked to dysfunction of ryanodine receptor (RyR)/intracellular calcium (Ca2+) release channels on the sarcoplasmic reticulum (SR). Mammalian skeletal muscle RyR1 channels undergo age-related remodeling due to oxidative overload, leading to loss of the stabilizing subunit calstabin1 (FKBP12) from the channel macromolecular complex. This destabilizes the closed state of the channel resulting in intracellular Ca2+ leak, reduced muscle function, and impaired exercise capacity. We now show that the C. elegans RyR homolog, UNC-68, exhibits a remarkable degree of evolutionary conservation with mammalian RyR channels and similar age-dependent dysfunction. Like RyR1 in mammals, UNC-68 encodes a protein that comprises a macromolecular complex which includes the calstabin1 homolog FKB-2 and is immunoreactive with antibodies raised against the RyR1 complex. Furthermore, as in aged mammals, UNC-68 is oxidized and depleted of FKB-2 in an age-dependent manner, resulting in ‘leaky’ channels, depleted SR Ca2+ stores, reduced body wall muscle Ca2+ transients, and age-dependent muscle weakness. FKB-2 (ok3007)-deficient worms exhibit reduced exercise capacity. Pharmacologically induced oxidization of UNC-68 and depletion of FKB-2 from the channel independently caused reduced body wall muscle Ca2+ transients. Preventing FKB-2 depletion from the UNC-68 macromolecular complex using the Rycal drug S107 improved muscle Ca2+ transients and function. Taken together, these data suggest that UNC-68 oxidation plays a role in age-dependent loss of muscle function. Remarkably, this age-dependent loss of muscle function induced by oxidative overload, which takes ~2 years in mice and ~80 years in humans, occurs in less than 2–3 weeks in C. elegans, suggesting that reduced antioxidant capacity may contribute to the differences in lifespan among species.

    1. Cell Biology
    Desiree Schatton et al.
    Research Article

    Proliferating cells undergo metabolic changes in synchrony with cell cycle progression and cell division. Mitochondria provide fuel, metabolites, and ATP during different phases of the cell cycle, however it is not completely understood how mitochondrial function and the cell cycle are coordinated. CLUH is a post-transcriptional regulator of mRNAs encoding mitochondrial proteins involved in oxidative phosphorylation and several metabolic pathways. Here, we show a role of CLUH in regulating the expression of astrin, which is involved in metaphase to anaphase progression, centrosome integrity, and mTORC1 inhibition. We find that CLUH binds both the SPAG5 mRNA and its product astrin, and controls the synthesis and the stability of the full-length astrin-1 isoform. We show that CLUH interacts with astrin-1 specifically during interphase. Astrin-depleted cells show mTORC1 hyperactivation and enhanced anabolism. On the other hand, cells lacking CLUH show decreased astrin levels and increased mTORC1 signaling, but cannot sustain anaplerotic and anabolic pathways. In absence of CLUH, cells fail to grow during G1, and progress faster through the cell cycle, indicating dysregulated matching of growth, metabolism and cell cycling. Our data reveal a role of CLUH in coupling growth signaling pathways and mitochondrial metabolism with cell cycle progression.