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

Martina Berardocco; Annalisa Radeghieri; Sara Busatto; Marialucia Gallorini; Chiara Raggi; Clarissa Gissi; Igea D’Agnano; Paolo Bergese; Armando Felsani; Anna C. Berardi

doi:10.18632/oncotarget.20503

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Research Papers:

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

Martina Berardocco, Annalisa Radeghieri, Sara Busatto, Marialucia Gallorini, Chiara Raggi, Clarissa Gissi, Igea D’Agnano, Paolo Bergese, Armando Felsani and Anna C. Berardi _

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Oncotarget. 2017; 8:82920-82939. https://doi.org/10.18632/oncotarget.20503

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Abstract

Martina Berardocco1, Annalisa Radeghieri2, Sara Busatto2, Marialucia Gallorini3, Chiara Raggi4, Clarissa Gissi1, Igea D’Agnano5, Paolo Bergese2, Armando Felsani5,6 and Anna C. Berardi1

1U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy

2Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy

3Department of Pharmacy, University G. d’Annunzio, Chieti, Italy

4Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano, Italy

5Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Italy

6Genomnia Srl, Bresso, Italy

Correspondence to:

Anna C. Berardi, email: [email protected], [email protected]

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.

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Research Papers:

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

Abstract