Non coding RNA expression by high throughput sequencing profiles of Extracellular Vesicles in human Hepatocellular carcinoma cell lines.

Introduction. Hepatocellular carcinoma (HCC) is one of the most common cancers with dismal clinical outcome accounting for the third highest cause of cancer related deaths worldwide. Recently, extracellular vesicles (EVs) have emerged as novel entity with a fascinating role in cancer progression. The current evidence suggests that further elucidation of EV function(s) may identify specific oncogenic markers that may be useful for diagnosis, prognosis and treatment of HCC where conventional therapies give unsatisfactory results. Here, we show that the extracellular vesicles released by HCC cell lines carry small non coding (nc) RNA. Materials and Methods. To define the contribution of the ncRNA cargo of HCC cell derived EVs we performed high throughput sequencing to identify different ncRNAs in the EVs. Using validated centrifugation protocols, we separated these EVs released by 4 different ECC cell lines Huh7, Huh6, HepG2 and Hep3B and performed RNA sequencing with the Applied Biosystems SOLiD Sequencer. Results. Various, but different, non-coding RNAs were detected in the EVs, including microRNA, tRNA, small nucleolar (sno)RNA, small nuclear (sn)RNA and lincRNA. We report the ncRNA composition of EVs released in the 4 HCC cell lines and the comparison of EVs ncRNA in the 4 different MVs derived HCC cell lines. Discussion. Significant differences in both miRNA and snoRNA expression profiles were found between MVs of the different HCC cell lines. Gene ontology analysis indicates that these ncRNAs target transcription factors and genes that participate in several cellular pathways, including angiogenesis, cellular transport, apoptosis, and proteolysis. Our data suggest that EVs transport gene regulatory information to modulate angiogenesis, and other cell pathways in recipient cells. Conclusions. These findings provided new insights into the characteristics of ncRNAs in extracellular vesicles derived from hepatocellular carcinoma cells and might become a new source for identification of the HCC markers.