RNA sequencing identifies specific PIWI-interacting small non-coding RNA expression patterns in breast cancer

// Adnan Hashim 1,* , Francesca Rizzo 1,* , Giovanna Marchese 1 , Maria Ravo 1 , Roberta Tarallo 1 , Giovanni Nassa 1 , Giorgio Giurato 1 , Gianluca Santamaria 1 , Angela Cordella 2 , Concita Cantarella 3 and Alessandro Weisz 1,4 1 Laboratory of Molecular Medicine and Genomics, Faculty of Medicine and Surgery, University of Salerno, Baronissi, SA, Italy 2 Fondazione IRCCS SDN, Napoli, Italy 3 Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per l’Orticoltura, Pontecagnano, SA, Italy 4 Division of Molecular Pathology and Medical Genomics, ‘SS. Giovanni di Dio e Ruggi d’Aragona' Hospital, University of Salerno, Salerno, Italy * These authors contributed equally to this work Correspondence: Alessandro Weisz, email: // Keywords : Breast cancer; PIWI; piRNAs; RNA-sequencing; Small non-coding RNA; Estrogen receptor Received : June 30, 2014 Accepted : September 15, 2014 Published : September 16, 2014 Abstract PIWI-interacting small non-coding RNAs (piRNAs) are genetic and epigenetic regulatory factors in germline cells, where they maintain genome stability, are involved in RNA silencing and regulate gene expression. We found that the piRNA biogenesis and effector pathway are present in human breast cancer (BC) cells and, analyzing smallRNA-Seq data generated from BC cell lines and tumor biopsies, we identified >100 BC piRNAs, including some very abundant and/or differentially expressed in mammary epithelial compared to BC cells, where this was influenced by estrogen or estrogen receptor β, and in cancer respect to normal breast tissues. A search for mRNAs targeted by the BC piRNome revealed that eight piRNAs showing a specific expression pattern in breast tumors target key cancer cell pathways. Evidence of an active piRNA pathway in BC suggests that these small non-coding RNAs do exert transcriptional and post-transcriptional gene regulatory actions also in cancer cells.