Single extracellular vesicle imaging via rolling circle amplification–expansion microscopy

Extracellular vesicles (EVs) from biological fluids can provide critical information for minimally invasive diagnostics and treatment monitoring, but their nanoscale size, low biomarker abundance, and heterogeneity pose challenges. Here, we integrate rolling circle amplification with expansion microscopy (RCA-ExM) to achieve super-resolution multi-omics profiling of single EVs using conventional fluorescence microscopy. Sensitive multimodal biomarker detection is achieved by employing RCA to detect switch hairpin probe-labeled EV membrane proteins, and EV-liposome fusion to detect EV miRNAs via delivery of specific molecular beacons and a signal-amplifying enzyme circuit. Next, hydrogel-mediated expansion is employed to enlarge the fused EVs to permit single-EV detections. RCA-ExM quantitation of miRNA-21 levels in EpCAM+ PD-L1+ plasma EVs from a clinical cohort (n = 86) successfully distinguishes cancer patients from healthy donors and differentiates 3 categories of immunotherapy efficacy. RCA-ExM therefore exhibits significant promise for more sensitive and specific diagnostics, and treatment monitoring applications.