Prostate cancer cell-derived extracellular vesicle subpopulations contain different gDNA fragments

Introduction: Extracellular vesicles (EVs) have an important role in the intercellular transfer of genetic information. EVs have been shown to contain nucleic acids such as mRNA, microRNAs, ncRNAs and even DNA. However, less is known of the genomic DNA (gDNA) packed into EVs. It is also unknown, whether the gDNA cargo is randomly sorted to the different EV subpopulations, or if it is preferably packed into specific vesicle types. The aim of this study was to analyse whether different prostate cancer (PCa) cell-derived EV subpopulations (apoptotic bodies, microvesicles and exosomes) carry different gDNA fragments. Methods: EV subpopulations from 3 PCa cell lines (LNCaP, PC-3 and RC92a/h) were separated by differential ultracentrifugation (1,200×g, 20,000×g and 110,000×g). The different EV subpopulations were verified through transmission electron microscopy and characterized by total protein content and nanoparticle tracking analysis (NTA). gDNA fragments of different genes were detected by qPCR and confirmed by DNA sequencing. Results: We report that the PCa EV subpopulations were different in terms of total protein and DNA content. Although the particle concentration of microvesicles and exosomes by NTA were similar, the total protein content was significantly different. Particle concentration and total protein content correlated with each other for some, but not all PCa cell-derived microvesicles and exosomes. Analysis of the gDNA content of TP53, PTEN and MLH1 fragments in the EV populations from the different PCa cell lines showed, that different EV subpopulations carry different gDNA content, which could indicate a selective mechanism of nucleic acid packing depending on the cell and the EV subtype. Summary/conclusion: PCa EV subpopulations carry different gDNA sequences, which could potentially be used as diagnostic and prognostic biomarkers.