Cardiac-immune microniches programme macrophage states in the regenerating heart

Abstract

Adult zebrafish regenerate their hearts after injury, a process that requires macrophages, yet how local tissue microenvironments instruct macrophage states and function remains unclear. Here we combine single cell RNA sequencing with Visium and high-resolution MERFISH spatial transcriptomics to map the cardio-immune landscape of homeostatic and regenerating zebrafish hearts. We identify a mpeg1.1+ compartment comprising macrophages, dendritic, B and NK-like cells, and show that injury establishes a macrophage-centred immune environment with transcriptional programmes spanning resident surveillance, damage sensing, inflammation, antigen presentation, resolution and metabolic support. Communication-aware spatial modelling reveals that these states are not randomly distributed but organised into discrete structural-immune microniches across the injury region, each defined by stereotyped cellular compositions and ligand-receptor circuits. Within a fibroblast-macrophage microniche, we uncover an il34-csf1ra-egr1 axis in which col12a1a+ il34+ fibroblasts promote an egr1 pro-regenerative macrophage state that couples fibrosis, vascular integrity and epicardial signalling. We show that disruption of this axis by csf1ra loss of function reduces macrophage-, endothelial- and epicardial-rich microniches, amplifying fibroblast-driven domains that shift macrophages towards stress and long-sustained inflammatory programmes, thereby biasing early injury response towards a pro-fibrotic state. Our work establishes spatially defined cardio-immune microniches as key organisers of macrophage function and regenerative outcome, providing a mechanistic framework and actionable targets for reprogramming cardiac repair.