RNA-seq reveals distinctive RNA profiles of small extracellular vesicles from different human liver cancer cell lines

// Martina Berardocco 1 , Annalisa Radeghieri 2 , Sara Busatto 2 , Marialucia Gallorini 3 , Chiara Raggi 4 , Clarissa Gissi 1 , Igea D’Agnano 5 , Paolo Bergese 2 , Armando Felsani 5, 6 and Anna C. Berardi 1 1 U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy 2 Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy 3 Department of Pharmacy, University G. d’Annunzio, Chieti, Italy 4 Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano, Italy 5 Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Italy 6 Genomnia Srl, Bresso, Italy Correspondence to: Anna C. Berardi, email: annacberardi@yahoo.it , annac.berardi@ausl.pe.it Keywords: extracellular vesicles, liver cancer, microRNA, small nucleolar RNA, RNA sequencing Received: February 10, 2017 Accepted: July 29, 2017 Published: August 24, 2017 ABSTRACT Liver cancer (LC) is one of the most common cancers and represents the third highest cause of cancer-related deaths worldwide. Extracellular vesicle (EVs) cargoes, which are selectively enriched in RNA, offer great promise for the diagnosis, prognosis and treatment of LC. Our study analyzed the RNA cargoes of EVs derived from 4 liver-cancer cell lines: HuH7, Hep3B, HepG2 (hepato-cellular carcinoma) and HuH6 (hepatoblastoma), generating two different sets of sequencing libraries for each. One library was size-selected for small RNAs and the other targeted the whole transcriptome. Here are reported genome wide data of the expression level of coding and non-coding transcripts, microRNAs, isomiRs and snoRNAs providing the first comprehensive overview of the extracellular-vesicle RNA cargo released from LC cell lines. The EV-RNA expression profiles of the four liver cancer cell lines share a similar background, but cell-specific features clearly emerge showing the marked heterogeneity of the EV-cargo among the individual cell lines, evident both for the coding and non-coding RNA species.