1. Cell Biology
  2. Computational and Systems Biology
Download icon

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
Research Article
  • Cited 118
  • Views 17,567
  • Annotations
Cite this article as: eLife 2019;8:e43882 doi: 10.7554/eLife.43882

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

  • 17,567
    Page views
  • 2,461
    Downloads
  • 118
    Citations

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

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)

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

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

Further reading

    1. Cell Biology
    Lisa M Strong et al.
    Research Article Updated

    Autophagy is a cellular process that degrades cytoplasmic cargo by engulfing it in a double-membrane vesicle, known as the autophagosome, and delivering it to the lysosome. The ATG12–5–16L1 complex is responsible for conjugating members of the ubiquitin-like ATG8 protein family to phosphatidylethanolamine in the growing autophagosomal membrane, known as the phagophore. ATG12–5–16L1 is recruited to the phagophore by a subset of the phosphatidylinositol 3-phosphate-binding seven-bladedß -propeller WIPI proteins. We determined the crystal structure of WIPI2d in complex with the WIPI2 interacting region (W2IR) of ATG16L1 comprising residues 207–230 at 1.85 Å resolution. The structure shows that the ATG16L1 W2IR adopts an alpha helical conformation and binds in an electropositive and hydrophobic groove between WIPI2 ß-propeller blades 2 and 3. Mutation of residues at the interface reduces or blocks the recruitment of ATG12–5–16 L1 and the conjugation of the ATG8 protein LC3B to synthetic membranes. Interface mutants show a decrease in starvation-induced autophagy. Comparisons across the four human WIPIs suggest that WIPI1 and 2 belong to a W2IR-binding subclass responsible for localizing ATG12–5–16 L1 and driving ATG8 lipidation, whilst WIPI3 and 4 belong to a second W34IR-binding subclass responsible for localizing ATG2, and so directing lipid supply to the nascent phagophore. The structure provides a framework for understanding the regulatory node connecting two central events in autophagy initiation, the action of the autophagic PI 3-kinase complex on the one hand and ATG8 lipidation on the other.

    1. Cell Biology
    Laura Le Pelletier et al.
    Research Article

    Aging is associated with central fat redistribution and insulin resistance. To identify age-related adipose features, we evaluated the senescence and adipogenic potential of adipose-derived-stromal cells (ASCs) from abdominal subcutaneous fat obtained from healthy normal-weight young (<25y) or older women (>60y). Increased cell passages of young-donor ASCs (in vitro aging), resulted in senescence but not oxidative stress. ASC-derived adipocytes presented impaired adipogenesis but no early mitochondrial dysfunction. Conversely, aged-donor ASCs at early passages displayed oxidative stress and mild senescence. ASC-derived adipocytes exhibited oxidative stress, and early mitochondrial dysfunction but adipogenesis was preserved. In vitro aging of aged-donor ASCs resulted in further increased senescence, mitochondrial dysfunction, oxidative stress and severe adipocyte dysfunction. When in vitro aged young-donor ASCs were treated with metformin, no alteration was alleviated. Conversely, metformin treatment of aged-donor ASCs decreased oxidative stress and mitochondrial dysfunction resulting in decreased senescence. Metformin's prevention of oxidative stress and of the resulting senescence improved the cells' adipogenic capacity and insulin sensitivity. This effect was mediated by the activation of AMP-activated-protein-kinase as revealed by its specific inhibition and activation. Overall, aging ASC-derived adipocytes presented impaired adipogenesis and insulin sensitivity. Targeting stress-induced senescence of ASCs with metformin may improve age-related adipose tissue dysfunction.