In vivo-compatible spatial multi-omics via hydrogen peroxide-independent APEX2 labeling

Proximity labeling (PL) technologies such as APEX2 have transformed spatial multi-omics in live cells, but their long-standing dependence on hydrogen peroxide (H₂O₂) disrupts redox signaling and prevents use in live animals. Here we introduce H₂O₂-independent APEX2 (Hi-APEX), which uses a clickable tetrazine-phenol (TP) probe, requiring no enzyme engineering. We show that APEX2 directly catalyzes TP labeling without H₂O₂ via a mechanism requiring the probe's tetrazine group and oxygen. We benchmark Hi-APEX-based spatial multi-omics by mapping the mitochondrial matrix and dynamic secretomes. Hi-APEX outperforms traditional APEX in capturing redox-sensitive processes such as stress response and ferroptosis, enabling the discovery of authentic stress granule components and protein interaction networks for mitochondria-localized GPX4 (mGPX4). One mGPX4 interactor, TRMT61B, which is known to regulate mitochondrial m¹A modifications, promotes ferroptosis. Crucially, Hi-APEX demonstrates in vivo compatibility, enabling direct protein and RNA PL in tumor xenografts and hippocampal neurons, thereby expanding PL-based spatial multi-omics from cellular systems to living organisms.