title: Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells--Evidence of unique microRNA cargos.
abstract: Melanoma cells release different types of extracellular vesicles (EVs) into the extracellular milieu that are involved with communication and signaling in the tumor microenvironment. Subsets of EVs include exosomes, microvesicles, and apoptotic bodies that carry protein and genetic (RNA) cargos. To define the contribution of the RNA cargo of melanoma cell derived EVs we performed small RNA sequencing to identify different small RNAs in the EV subsets. Using validated centrifugation protocols, we separated these EV subsets released by the melanoma cell line MML-1, and performed RNA sequencing with the Ion Torrent platform. Various, but different, non-coding RNAs were detected in the EV subsets, including microRNA, mitochondrial associated tRNA, small nucleolar RNA, small nuclear RNA, Ro associated Y-RNA, vault RNA and Y-RNA. We identified in total 1041 miRNAs in cells and EV subsets. Hierarchical clustering showed enrichment of specific miRNAs in exosomes, including hsa-miR-214-3p, hsa-miR-199a-3p and hsa-miR-155-5p, all being associated with melanoma progression. Comparison of exosomal miRNAs with miRNAs in clinical melanoma samples indicate that multiple miRNAs in exosomes also are expressed specifically in melanoma tissues, but not in benign naevi. This study shows for the first time the presence of distinct small RNAs in subsets of EVs released by melanoma cells, with significant similarities to clinical melanoma tissue, and provides unique insights into the contribution of EV associated extracellular RNA in cancer.
authors.affiliation: a Krefting Research Center ; Institute of Medicine; University of Gothenburg ; Gothenburg , Sweden.
authors.forename: Taral R
authors.initials: TR
authors.lastname: Lunavat
authors.forename: Lesley
authors.initials: L
authors.lastname: Cheng
authors.forename: Dae-Kyum
authors.initials: DK
authors.lastname: Kim
authors.forename: Joydeep
authors.initials: J
authors.lastname: Bhadury
authors.forename: Su Chul
authors.initials: SC
authors.lastname: Jang
authors.forename: Cecilia
authors.initials: C
authors.lastname: Lässer
authors.forename: Robyn A
authors.initials: RA
authors.lastname: Sharples
authors.forename: Marcela Dávila
authors.initials: MD
authors.lastname: López
authors.forename: Jonas
authors.initials: J
authors.lastname: Nilsson
authors.forename: Yong Song
authors.initials: YS
authors.lastname: Gho
authors.forename: Andrew F
authors.initials: AF
authors.lastname: Hill
authors.forename: Jan
authors.initials: J
authors.lastname: Lötvall
mesh_terms: D015153:Blotting, Western; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D018450:Disease Progression; D055354:Exosomes / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D000067128:Extracellular Vesicles / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008545:Melanoma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D035683:MicroRNAs / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D046529:Microscopy, Electron, Transmission; D020411:Oligonucleotide Array Sequence Analysis; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000145:classification / Q000235:genetics*
chemical_list: C505361:MIRN15 microRNA, human; C547397:MIRN214 microRNA, human; D035683:MicroRNAs; D058727:RNA, Small Untranslated; C531408:mirn199 microRNA, human
keywords: cancer; extracellular RNA; malignant melanoma; membrane vesicles; next-generation sequencing; non-coding RNA