Abstract

Zebrafish have the remarkable ability to regenerate their heart after injury. Macrophages are critical in this process: they clear up dead cells and debris, participate in fibrosis but also contribute to regeneration through interactions with their tissue microenvironment. However, little is known about the precise regulation shaping macrophage identity and function in response to cardiac injury. By combining single-cell and spatial transcriptomics, we discovered the composition and activation states of various immune cell populations found in distinct spatial territories of the regenerating and homeostatic heart. We uncovered information about macrophage, dendritic, B and NK cell transcriptomes and their correspondent location within the cardiac tissue, including the epicardium, the outflow tract, as well as the injury-zone cardiomyocyte microenvironment. By reconstructing immune-related cellular niches across the regenerating and the homeostatic heart, we were able to discover the molecular signatures mediating such specific cell-cell communication, therefore contributing towards dissecting the regulatory programmes driving macrophage pro-fibrotic and pro-regenerative phenotypes. Further analysis is underway to understand how specific microenvironmental signaling interactions may be enhanced or disrupted to support tissue regeneration. Our findings reveal how knowledge of cardiac niche-specific immune interactions could guide more effective pro-regenerative and anti-fibrotic therapies.