Comparative single-cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration

  1. Ke-Hsuan Wei
  2. I-Ting Lin
  3. Kaushik Chowdhury
  4. Khai Lone Lim
  5. Kuan-Ting Liu
  6. Tai-Ming Ko
  7. Yao-Ming Chang
  8. Kai-Chien Yang
  9. Shih-Lei Lai  Is a corresponding author
  1. Institute of Biomedical Sciences, Academia Sinica, Taiwan
  2. National Yang Ming Chiao Tung University, Taiwan
  3. National Taiwan University, Taiwan

Abstract

Zebrafish exhibit a robust ability to regenerate their hearts following injury, and the immune system plays a key role in this process. We previously showed that delaying macrophage recruitment by clodronate liposome (-1d_CL, macrophage-delayed model) impairs neutrophil resolution and heart regeneration, even when the infiltrating macrophage number was restored within the first-week post injury (Lai et al., 2017). It is thus intriguing to learn the regenerative macrophage property by comparing these late macrophages vs. control macrophages during cardiac repair. Here, we further investigate the mechanistic insights of heart regeneration by comparing the non-regenerative macrophage-delayed model with regenerative controls. Temporal RNAseq analyses revealed that -1d_CL treatment led to disrupted inflammatory resolution, ROS homeostasis, and energy metabolism during cardiac repair. Comparative single-cell RNAseq profiling of inflammatory cells from regenerative vs. non-regenerative hearts further identified heterogeneous macrophages and neutrophils, showing alternative activation and cellular crosstalk leading to neutrophil retention and chronic inflammation. Among macrophages, two residential subpopulations (hbaa+ Mac 2 and timp4.3+ Mac 3) were enriched only in regenerative hearts and barely recovered after -1d_CL treatment. To deplete the resident macrophage without delaying the circulating macrophage recruitment, we established the resident macrophage-deficient model by administrating CL earlier at 8 days (-8d_CL) before cryoinjury. Strikingly, resident macrophage-deficient zebrafish still exhibited defects in revascularization, cardiomyocyte survival, debris clearance, and ECM remodeling/scar resolution without functional compensation from the circulating/monocyte-derived macrophages. Our results characterized the diverse function and interaction between inflammatory cells and identified unique resident macrophages prerequisite for zebrafish heart regeneration.

Data availability

All data generated or analyzed during this study have been included in the manuscript and uploaded to a public entry for raw reads of both bulk and single-cell RNAseq on NCBI SRA database (accession no. PRJNA900299). Source data files of respective figures have been provided.

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

Article and author information

Author details

  1. Ke-Hsuan Wei

    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
    Competing interests
    The authors declare that no competing interests exist.
  2. I-Ting Lin

    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
    Competing interests
    The authors declare that no competing interests exist.
  3. Kaushik Chowdhury

    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
    Competing interests
    The authors declare that no competing interests exist.
  4. Khai Lone Lim

    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
    Competing interests
    The authors declare that no competing interests exist.
  5. Kuan-Ting Liu

    Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Taipei, Taiwan
    Competing interests
    The authors declare that no competing interests exist.
  6. Tai-Ming Ko

    Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Taipei, Taiwan
    Competing interests
    The authors declare that no competing interests exist.
  7. Yao-Ming Chang

    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
    Competing interests
    The authors declare that no competing interests exist.
  8. Kai-Chien Yang

    Department and Graduate Institute of Pharmacology, National Taiwan University, Taipei, Taiwan
    Competing interests
    The authors declare that no competing interests exist.
  9. Shih-Lei Lai

    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
    For correspondence
    ben.s.lai@ibms.sinica.edu.tw
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1409-4701

Funding

Institute of Biomedical Sciences, Academia Sinica (IBMS-CRC108-P01)

  • Shih-Lei Lai

Ministry of Science and Technology, Taiwan (MOST 108-2320-B-001-032-MY2)

  • Shih-Lei Lai

Academia Sinica (AS-GC-110-P7)

  • Shih-Lei Lai

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

Reviewing Editor

  1. Marianne E Bronner, California Institute of Technology, United States

Ethics

Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the Academia Sinica. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols (Protocol ID: 18-12-1241) of Academia Sinica. The protocol was approved by the Committee on the Ethics of Animal Experiments of the Academia Sinica. All surgery was performed under tricaine anesthesia, and every effort was made to minimize suffering.

Version history

  1. Preprint posted: November 22, 2022 (view preprint)
  2. Received: November 22, 2022
  3. Accepted: July 26, 2023
  4. Accepted Manuscript published: July 27, 2023 (version 1)
  5. Version of Record published: August 9, 2023 (version 2)

Copyright

© 2023, Wei 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.

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  1. Ke-Hsuan Wei
  2. I-Ting Lin
  3. Kaushik Chowdhury
  4. Khai Lone Lim
  5. Kuan-Ting Liu
  6. Tai-Ming Ko
  7. Yao-Ming Chang
  8. Kai-Chien Yang
  9. Shih-Lei Lai
(2023)
Comparative single-cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration
eLife 12:e84679.
https://doi.org/10.7554/eLife.84679

Share this article

https://doi.org/10.7554/eLife.84679

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