Near-infrared photochromic miniprotein enables photoacoustic molecular imaging of acute inflammation and intracellular antigens.

Using near-infrared photoswitchable photochromic genetically encoded probes, differential photoacoustic tomography (PAT) enables deep-tissue imaging with high resolution and sensitivity; however, current bacteriophytochrome-based probes are bulky multidomain proteins exceeding 55 kDa, which constrains their use for designing PAT molecular reporters. Here we engineer rsmiRFPnano, a compact cyanobacteriochrome-derived photoswitchable PAT probe. With a molecular weight below 19 kDa, rsmiRFPnano efficiently incorporates biliverdin, exhibits high extinction coefficients in both photochromic states and demonstrates robust performance in live cells. We established rsmiRFPnano-based reporters for NF-κB and AP-1 pathways, which display low basal activity and strong activation-dependent responses. These reporters effectively visualized acute inflammation using noninvasive PAT in vivo, further validated through cellular-level spatial omics mapping. We then created photoswitchable nanobody probes, rsNIR-Fbs, stabilized upon antigen binding and rapidly degraded otherwise, enabling selective photoacoustic immuno-imaging of intracellular antigens in vivo. Together, these results establish rsmiRFPnano as an ultracompact and versatile platform for molecular PAT.