Non-destructive colocalization sensing of microRNAs and membrane proteins in single vesicles reveals spatial inflammation signatures

Chronic inflammation underlies a broad spectrum of diseases, yet current liquid biopsy approaches lack the spatial resolution and molecular specificity to detect localized, disease-specific inflammatory signals. Extracellular vesicles (EVs) offer a promising alternative, as they carry both membrane proteins and intravesicular biomolecules that reflect the physiological state and tissue of origin. Here, we present a sensing platform for single-vesicle colocalization analysis of membrane proteins and microRNAs (miRNAs), using cellulose nanofiber-mediated membrane fusion to non-destructively deliver probes into intact EVs. This approach enables simultaneous detection of tissue-specific and inflammation-associated markers in individual EVs. In kidney transplant recipients with chronic active antibody-mediated rejection, we identify EVs co-expressing the renal marker DPYS and miR-1246. In rheumatoid arthritis patients, we observe elevated levels of miR-1246 + /CD81 + EVs in plasma. Our platform distinguishes among inflammation-related EV subpopulations that are undetectable using bulk or surface-only analyses, thereby offering a non-invasive strategy for localized inflammation profiling.