Isolation and Analysis of MicroRNAs from Extracellular Vesicles of the Parasitic Model Nematodes Nippostrongylus brasiliensis and Trichuris muris

The identification, detection, and use of small RNA species have rapidly gained interest—especially to study parasite–host interactions. Parasite-to-host communication is contributed by small secreted extracellular vesicle (EV)-derived nucleic acid species. In particular, microRNAs (miRNAs) and small interfering RNAs can regulate the host response by targeting cells at both transcriptional and posttranscriptional levels. Here, modified protocols for density gradient purification of EVs from nematodes and the subsequent extraction of EV-derived small RNAs using commercially available reagents and kits are provided with a special focus on basic background information. Further, considerations for Next-Generation Sequencing using the Illumina NextSeq500 sequencing technology (kit-based library preparation, small RNA sequencing, and miRNA sequence analysis pipelines using the miRDeep2 package) are introduced. Key words MicroRNA identification miRNA Extracellular vesicles EV Helminths Parasite–host interaction Parasite Nematode Nippostrongylus brasiliensis Trichuris muris Hookworm Whipworm NextSeq500 miRDeep2 packag