Widespread and Functional RNA Circularization in Localized Prostate Cancer

The cancer transcriptome is remarkably complex, including low-abundance transcripts, many not polyadenylated. To fully characterize the transcriptome of localized prostate cancer, we performed ultra-deep total RNA-seq on 144 tumors with rich clinical annotation. This revealed a linear transcriptomic subtype associated with the aggressive intraductal carcinoma sub-histology and a fusion profile that differentiates localized from metastatic disease. Analysis of back-splicing events showed widespread RNA circularization, with the average tumor expressing 7,232 circular RNAs (circRNAs). The degree of circRNA production was correlated to disease progression in multiple patient cohorts. Loss-of-function screening identified 11.3% of highly abundant circRNAs as essential for cell proliferation; for ∼90% of these, their parental linear transcripts were not essential. Individual circRNAs can have distinct functions, with circCSNK1G3 promoting cell growth by interacting with miR-181. These data advocate for adoption of ultra-deep RNA-seq without poly-A selection to interrogate both linear and circular transcriptomes. [Display omitted] •Ultra-deep rRNA-depleted RNA sequencing of 144 localized prostate tumors•Fusion gene profiles differentiate localized from metastatic disease•Widespread RNA circularization events define clinically distinct tumor subtypes•Functional screening reveals pervasive circular isoform-specific essentiality RNA circularization is a pervasive feature of prostate cancer, with hundreds of circRNAs promoting cell proliferation through functions distinct from their parental linear RNA.