Quantifying full-length circular RNAs in cancer

Circular RNAs (circRNAs) have been found abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with with different types of biomolecules. Alternative splicing can create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels using RNA sequencing data. We confirm the effectiveness and computational efficiency of psirc using both simulated and actual experimental data. Applying psirc on transcriptome profiles from nasopharyngeal carcinoma and normal nasopharynx samples, we discovered circRNA isoforms differentially expressed between the two groups. Compared to the assumed circular isoforms derived from linear transcript annotations, some of the alternatively spliced circular isoforms have 100 times higher expression and contain fewer microRNA response elements, demonstrating the importance of quantifying full-length circRNA isoforms. Four immortalized normal nasopharyngeal epithelial cell lines (NP69, NP361, NP460 and NPC550), 2 EBV-positive NPC cell lines (C666-1 and NPC43), 7 patient-derived xenografts (Xeno-666, Xeno-2117, Xeno-1915, Xeno-99186, C15, C17 and Xeno-32) and 2 patient tumor specimens (NPC-M1 and NPC-M2) were used in this study.