Identification of Specific PIWI-interacting Small Noncoding RNA (piRNA) Expression Patterns During Hepatocarcinogenesis

Background: Hepatocellular carcinoma (HCC) is the most frequent primary liver malignancy, mostly occurring in the context of chronic liver diseases leading to cirrhosis, more often beginning with development of premalignant lesions, characterized by low- (LGDN) and high-grade (HGDN) dysplastic nodules. P-element induced Wimpy testis (PIWI)- interacting RNAs (piRNAs) represent a large family of small noncoding RNAs, 23-35 nucleotide-long, first identified in fruitfly germline cells by their ability to interact with PIWI proteins and thereby exert epigenetic silencing of retrotransposons. The piRNAs are now also known as post-transcriptional regulators in somatic tissues, including stem and cancer cells, where piRNAs and piRNA-like molecules have been shown to influence key cellular processes. Methods: We applied small RNA sequencing to search for liver piRNAs and to profile their expression patterns in cirrhotic nodules (CNs), LGDN, HGDN, early HCC and progressed HCC (pHCC), analyzing 55 nodules from 17 patients. Results: We identified an expression signature of 58 piRNAs and 67 novel piRNA-like molecules that clearly discriminates HCC from matched CNs, correlating also to clinicopathological characteristics of HCC. This result was confirmed by functional analysis of predicted piRNA target mRNAs. Interestingly, 24 piRNAs showed specific expression patterns in dysplastic nodules compared to cirrhotic liver and/or pHCC. Conclusions: These results demonstrate that the piRNA pathway is active in human liver, where it is likely to represent a new player in the molecular events that characterize hepatocellular carcinogenesis, from early stages to pHCC. Furthermore, they suggest that piRNAs might represent new disease biomarkers, potentially useful for differential diagnosis of dysplastic and neoplastic liver lesions.