Identification of tumorigenesis-related mRNAs associated with RNA-binding protein HuR in thyroid cancer cells

// Federica Baldan 1 , Catia Mio 1 , Lorenzo Allegri 1 , Ketty Conzatti 1 , Barbara Toffoletto 1 , Cinzia Puppin 1 , Slobodanka Radovic 2 , Carlo Vascotto 1 , Diego Russo 3 , Carla Di Loreto 1, 4 , Giuseppe Damante 1, 5 1 Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy 2 IGA Technology Services Srl, 33100 Udine, Italy 3 Department of Health Sciences, University of Catanzaro “Magna Graecia”, 88100 Catanzaro, Italy 4 Institute of Anatomic Pathology, University Hospital “S. Maria della Misericordia”, 33100 Udine, Italy 5 Institute of Medical Genetics, University Hospital “S. Maria della Misericordia”, 33100 Udine, Italy Correspondence to: Giuseppe Damante, email: giuseppe.damante@uniud.it Keywords: HuR, RNA-binding proteins, RNA-seq, RIP-seq Received: December 21, 2015 Accepted: July 26, 2016 Published: August 12, 2016 ABSTRACT RNA binding proteins (RBPs) play a central role in cell physiology and pathology. Among them, HuR is a nuclear RBP, which shuttles to the cytoplasm to allow its RNA targets processing. HuR over-expression and delocalization are often associated to cell transformation. Numerous cancers display increased HuR protein levels and its high cytoplasmic levels has been associated with a worse prognosis. In our study, we first evaluated HuR expression in normal and cancer thyroid tissues and then evaluated its function in thyroid cell lines. HuR is over-expressed in all thyroid tumor tissues; high cytoplasmic levels are detected in all thyroid carcinomas. HuR silencing decreased cell viability and determined apoptotic cell death, in a non-tumorigenic (Nthy-ori-3.1) and a tumorigenic (BCPAP) thyroid cell line. Global transcriptome analysis indicated that HuR silencing, though having similar biological effects, induces distinct gene expression modifications in the two cell lines. By using the RIP-seq approach, the HuR-bound RNA profiles of different thyroid cell lines were evaluated. We show that in distinct cell lines HuR-bound RNA profiles are different. A set of 114 HuR-bound RNAs distinguishing tumorigenic cell lines from the non-tumorigenic one was identified. Altogether, our data indicate that HuR plays a role in thyroid tumorigenesis. Moreover, our findings are a proof of concept that RBP targets differ between cells with the same origin but with distinct biological behavior.