"The Landscape of Circular RNA in Cancer"
Circular RNAs (circRNA) are a new class of abundant, non-adenylated, and stable RNAs that form a covalently closed loop. Recent studies have suggested that circRNAs play important regulatory roles through interactions with miRNAs and ribonucleoproteins. High-throughput RNA-sequencing to detect circRNAs requires non-poly(A) selected protocols. In this study, we established the use of Exome Capture RNA-Seq protocol to profile circRNAs across more than 1000 human cancers samples. We validated our protocol against two other gold-standard methods, depletion of rRNA (Ribo-Zero) and digestion of linear transcripts (RNase-R). Capture RNA-seq was shown to greatly facilitate the high-throughput profiling of circRNAs, providing the most comprehensive catalogue of circRNA species to-date. Specifically, our method achieved significantly better enrichment for circRNAs than rRNA depletion, and, unlike RNase-R treatment, preserved accurate circular-to-linear ratios. Although the correlation between circular and linear isoform abundance was modest in general, we found strong evidence that the lineage specificity of circular RNAs is due to the lineage specificity of their parent genes. To shed light on the mechanism of circRNAs biogenesis, we are investigating the associations between mutations in canonical splicing sites and splicing factors with aberrant formation of circRNAs. The ratio of circular to linear transcript abundance was also explored to give insight into the dynamics between transcriptome stability/turnover and cell proliferation. Last but not least, we argued that a well-curated database of circRNA would help to distinguish circRNAs from certain genomic rearrangements in cancer that might mimic back-splicing events, namely Partial Tandem Duplication (PTD). Overall, our compendium provides a comprehensive resource that could aid in the exploration of circRNAs as a new type of biomarker, or as intriguing splicing and regulatory phenomena.