In vivo single-cell RNA metabolic labeling resolves early transcriptional responders in the regenerating zebrafish heart
- Janita Mintcheva
- Tzu-Lun Tseng
- Pinelopi Goumenaki
- Anika Neuschulz
- Anis Senoussi
- Sara Lelek
- Khai Lone Lim
- Zhitao Ming
- Ronny Schäfer
- Alisa Hnatiuk
- Nikolay Ninov
- Arica Beisaw
- Maura McGrail
- Shih-Lei Ben Lai
- Daniela Panáková
- Didier Y. R. Stainier
- Jan Philipp Junker
2026-05-05
The adult zebrafish heart can regenerate after injury, but the earliest gene expression changes that trigger this process remain poorly understood. Here we show that in vivo single-cell RNA metabolic labeling, which marks newly made RNA in individual cells, can capture rapid responses in the adult zebrafish heart after injury. Within the first 6 h, we detect activation of innate immune programs, including Toll-like receptor signaling, in a subset of macrophage-like immune cells. Analysis of a larger single-cell dataset indicates that neutrophils also contribute to this early response. Guided by these data, we show that macrophage-specific inhibition of the Toll-like receptor adaptor MyD88 reduces the pro-inflammatory macrophage response at the injury site and improves early hallmarks of regeneration. Our work establishes RNA metabolic labeling as a useful approach for measuring acute responses in vivo at single-cell resolution and identifies early immune-cell activation as a tunable component of heart regeneration.