Characterization of the microRNA transcriptomes and proteomics of cochlear tissue-derived small extracellular vesicles from mice of different ages after birth

The study of extracellular vesicles (EVs) has the potential to identify unknown cellular and molecular mechanisms in intercellular communication and in organ homeostasis and disease. Exosomes, with an average diameter of ~100 nanometers, are a subset of EVs. The biogenesis of exosomes involves their origin in endosomes, and subsequent interactions with other intracellular vesicles and organelles generate the final content of the exosomes. Their diverse constituents include nucleic acids, proteins, lipids, amino acids, and metabolites, which can reflect their cell of origin. In various diseases, exosomes offer a window into altered cellular or tissue states, and their detection in biological fluids potentially offers a multicomponent diagnostic readout. The efficient exchange of cellular components through exosomes can inform their applied use in designing exosome-based therapeutics.

Exosomes are small, single-membrane, secreted organelles of ∼30 to ∼200 nm in diameter that have the same topology as the cell and are enriched in selected proteins, lipids, nucleic acids, and glycoconjugates. Exosomes contain an array of membrane-associated, high-order oligomeric protein complexes, display pronounced molecular heterogeneity, and are created by budding at both plasma and endosome membranes. Exosome biogenesis is a mechanism of protein quality control, and once released, exosomes have activities as diverse as remodeling the extracellular matrix and transmitting signals and molecules to other cells. This pathway of intercellular vesicle traffic plays important roles in many aspects of human health and disease, including development, immunity, tissue homeostasis, cancer, and neurodegenerative diseases. In addition, viruses co-opt exosome biogenesis pathways both for assembling infectious particles and for establishing host permissiveness. On the basis of these and other properties, exosomes are being developed as therapeutic agents in multiple disease models.

The functional characterization of miRNAs is still an open challenge. Here, we present DIANA-miRPath v3.0 (http://www.microrna.gr/miRPathv3) an online software suite dedicated to the assessment of miRNA regulatory roles and the identification of controlled pathways. The new miRPath web server renders possible the functional annotation of one or more miRNAs using standard (hypergeometric distributions), unbiased empirical distributions and/or meta-analysis statistics. DIANA-miRPath v3.0 database and functionality have been significantly extended to support all analyses for KEGG molecular pathways, as well as multiple slices of Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio). Importantly, more than 600 000 experimentally supported miRNA targets from DIANA-TarBase v7.0 have been incorporated into the new schema. Users of DIANA-miRPath v3.0 can harness this wealth of information and substitute or combine the available in silico predicted targets from DIANA-microT-CDS and/or TargetScan v6.2 with high quality experimentally supported interactions. A unique feature of DIANA-miRPath v3.0 is its redesigned Reverse Search module, which enables users to identify and visualize miRNAs significantly controlling selected pathways or belonging to specific GO categories based on in silico or experimental data. DIANA-miRPath v3.0 is freely available to all users without any login requirement.