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

Ke-Hsuan Wei; I-Ting Lin; Kaushik Chowdhury; Khai Lone Lim; Kuan-Ting Liu; Tai-Ming Ko; Yao-Ming Chang; Kai-Chien Yang; Shih-Lei Ben Lai

doi:10.7554/eLife.84679

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

Elife. 2023 Jul 27:12:e84679. doi: 10.7554/eLife.84679.

Authors

Ke-Hsuan Wei^{1

2}, I-Ting Lin², Kaushik Chowdhury^{2

3}, Khai Lone Lim^{2

3}, Kuan-Ting Liu⁴, Tai-Ming Ko^{2

4}, Yao-Ming Chang², Kai-Chien Yang^{2

5}, Shih-Lei Ben Lai^{1

2

3}

Affiliations

¹ Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.
² Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
³ Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
⁴ Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Taipei, Taiwan.
⁵ Department and Graduate Institute of Pharmacology, National Taiwan University College of Medicine, Taipei, 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, reactive oxygen species 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 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 d (-8d_CL) before cryoinjury. Strikingly, resident macrophage-deficient zebrafish still exhibited defects in revascularization, cardiomyocyte survival, debris clearance, and extracellular matrix 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.

Keywords: comparative analysis; developmental biology; heart regeneration; immune response; macrophages; myocardial infarction; scRNAseq; zebrafish.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cicatrix / pathology
Heart* / physiology
Inflammation / pathology
Macrophages / metabolism
Myocytes, Cardiac / metabolism
Zebrafish* / physiology

Grants and funding

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