Discrimination between vesicular and nonvesicular extracellular tRNAs and their fragments

The extracellular space contains RNAs both inside and outside extracellular vesicles (EVs). Among RNA types, tRNAs and tRNA-derived small RNAs (tDRs) tend to be abundant and are frequently detected when performing small RNA sequencing of extracellular samples. For several applications, including answering basic biology questions and biomarker discovery, it is important to understand which specific extracellular tRNAs and tDRs are inside EVs and which are not. We have observed that EVs contain mainly full-length tRNAs, while cells also release full-length tRNAs into nonvesicular fractions. However, these nonvesicular tRNAs are fragmented by extracellular ribonucleases into nicked tRNAs, which can dissociate into tDRs both in extracellular samples and in the laboratory. It is therefore crucial to separate EVs from other nonvesicular RNA-containing extracellular carriers to prevent cross-contamination. Otherwise, extracellular tDR profiling may mix up signals coming from structurally and functionally different carrier types. Here, we provide two protocols that achieve this by: (a) density gradient separation and, (b) the use of commercial, pre-packed size-exclusion chromatography columns. The first protocol is time-consuming but achieves high resolution, while the second protocol is faster, simpler, and recommended for routine separations. Taken together, they form a solid experimental toolkit for addressing different questions related to extracellular tRNA biology or biomarker discovery.