Read-through transcripts in normal human lung parenchyma are down-regulated in lung adenocarcinoma.

// Giulia Pintarelli 1, * , Alice Dassano 1, * , Chiara E. Cotroneo 1, 6 , Antonella Galvan 7 , Sara Noci 1 , Rocco Piazza 2, 3 , Alessandra Pirola 2 , Roberta Spinelli 8 , Matteo Incarbone 4 , Alessandro Palleschi 5 , Lorenzo Rosso 5 , Luigi Santambrogio 5 , Tommaso A. Dragani 1 , Francesca Colombo 1 1 Department of Predictive and Prevention Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy 2 Department of Health Sciences, University of Milano-Bicocca, Monza, Italy 3 Hematology and Clinical Research Unit, San Gerardo Hospital, Monza, Italy 4 Department of Surgery, San Giuseppe Hospital, Multimedica, Milan, Italy 5 Department of Surgery, IRCCS Fondazione Ca Granda Ospedale Maggiore Policlinico, Universita degli Studi di Milano, Milan, Italy 6 Present Address: UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland 7 Formerly, Department of Predictive and Prevention Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy 8 Formerly, Department of Health Sciences, University of Milano-Bicocca, Monza, Italy * These authors have contributed equally to this work Correspondence to: Tommaso A. Dragani, e-mail: tommaso.dragani@istitutotumori.mi.it Keywords: conjoined genes, gene fusion, lung adenocarcinoma, RNA-Seq, read-through transcripts Received: November 17, 2015      Accepted: February 18, 2016      Published: April 02, 2016 ABSTRACT Read-through transcripts result from the continuous transcription of adjacent, similarly oriented genes, with the splicing out of the intergenic region. They have been found in several neoplastic and normal tissues, but their pathophysiological significance is unclear. We used high-throughput sequencing of cDNA fragments (RNA-Seq) to identify read-through transcripts in the non-involved lung tissue of 64 surgically treated lung adenocarcinoma patients. A total of 52 distinct read-through species was identified, with 24 patients having at least one read-through event, up to a maximum of 17 such transcripts in one patient. Sanger sequencing validated 28 of these transcripts and identified an additional 15, for a total of 43 distinct read-through events involving 35 gene pairs. Expression levels of 10 validated read-through transcripts were measured by quantitative PCR in pairs of matched non-involved lung tissue and lung adenocarcinoma tissue from 45 patients. Higher expression levels were observed in normal lung tissue than in the tumor counterpart, with median relative quantification ratios between normal and tumor varying from 1.90 to 7.78; the difference was statistically significant ( P < 0.001, Wilcoxon’s signed-rank test for paired samples) for eight transcripts: ELAVL1–TIMM44, FAM162B–ZUFSP, IFNAR2–IL10RB, INMT–FAM188B, KIAA1841–C2orf74, NFATC3–PLA2G15, SIRPB1–SIRPD , and SHANK3–ACR . This report documents the presence of read-through transcripts in apparently normal lung tissue, with inter-individual differences in patterns and abundance. It also shows their down-regulation in tumors, suggesting that these chimeric transcripts may function as tumor suppressors in lung tissue.