Bioluminescence-activated proximity labeling for spatial multi-omics

Abstract

Mapping the spatial organization of proteins and cellular interactions is crucial for understanding their biological functions. Herein, we report a biocompatible, multi-functional luminescence-activated proximity labeling (LAP) strategy for profiling subcellular proteomes and cell-cell interactions in live cells and animals. Our method capitalizes on fusing the photocatalyst miniSOG to NanoLuc luciferase, whose bioluminescence activates miniSOG via a resonance energy transfer mechanism, generating reactive oxygen species in situ to mediate proximity labeling (PL). We demonstrated the high spatial specificity of LAP in a C57BL6/N mouse model transplanted with MC38 cells. Our data revealed tumor microenvironment-dependent remodeling of secretome. LAP was further applied to identify ligand-receptor-mediated cell-cell interactions both in vitro and in vivo. We also achieved local transcriptome profiling by combining LAP with next-generation sequencing. Overall, LAP was proved to be a versatile PL technique with strong biocompatibility for spatial multi-omic applications.