Simultaneous protein and RNA analysis in single extracellular vesicles, including viruses: SPIRFISH

Interest in using nanoparticles for delivery of therapeutic RNA has been steadily growing, provoking a need to precisely understand their structure and contents. Single-particle and single-molecule analysis techniques provide snapshots of single biological nanoparticles, including viruses, liposomes, and extracellular vesicles (EVs). While existing methods primarily focus on protein detection, RNA delivery is becoming increasingly prevalent. A method to simultaneously detect protein and internal RNA in the same particle would reveal variability in size, structure, and RNA packaging efficiency, enabling optimization of nanoparticle delivery. Here, we introduce SPIRFISH, a high-throughput method for single-particle protein and RNA analysis, combining single particle interferometric reflectance imaging sensor (SP-IRIS) with single-molecule fluorescence in-situ hybridization (smFISH). Using SPIRFISH, we detect HIV-1 envelope protein and genomic RNA within single infectious virions, allowing resolution against EV background and noninfectious virions. We further show that SPIRFISH can be used to detect specific RNA within EVs. SPIRFISH should enable single particle analysis of a broad class of RNA-containing nanoparticles. ### Competing Interest Statement Kenneth W Witwer is or has been an advisory board member of ShiftBio, Exopharm, NeuroDex, NovaDip, and ReNeuron; holds NeuroDex options; privately consults as Kenneth Witwer Consulting. Zach Troyer, Mona Batish, and Kenneth W Witwer conduct research under a sponsored research agreement with Ionis Pharmaceuticals. Michael B Elowitz is a scientific advisory board member or consultant at TeraCyte, Primordium, and Spatial Genomics. All other authors declare they have no competing interests