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.
Highlights
Several genetic alterations have been reported to act as driver events in lung tumorigenesis or to modulate the progression of lung tumors and their responses to therapy [1, 2]
Evidence for read‐through transcripts is currently limited to our incidental discovery, during a gene expression study, of RNA chimeras formed by the intergenic transcription of the conjoined genes PPP3R1 and CNRIP1, in a few samples of lung adenocarcinoma and normal lung tissue [19]
The RNA‐Seq data were analyzed to identify chimeric transcripts involving two adjacent genes on the same chromosome, in the same orientation. This criterion, together with the fact that the RNA samples were from apparently normal tissue, maximized the probability that the identified chimeric transcripts had been generated by transcriptional read‐through events, without genetic aberrations
Summary
Several genetic alterations have been reported to act as driver events in lung tumorigenesis or to modulate the progression of lung tumors and their responses to therapy [1, 2] Among these alterations, chromosomal rearrangements (e.g. translocations, inversions and insertions) affecting genes encoding receptor tyrosine kinases, such as ALK, ROS1 and RET, have been extensively studied [1, 3,4,5,6,7,8,9]. The identification of read‐through transcripts has been made easier by the possibility of transcriptome sequencing using ‐generation technologies [11] Through this approach, read‐through transcripts have been observed in several tumor types, such as breast, prostate, gastric, and renal cancer [12,13,14,15,16,17,18]. Evidence for read‐through transcripts is currently limited to our incidental discovery, during a gene expression study, of RNA chimeras formed by the intergenic transcription of the conjoined genes PPP3R1 and CNRIP1, in a few samples of lung adenocarcinoma and normal lung tissue [19]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
