Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer

Asta M Rasmussen; Trine Line H Okholm; Michael Knudsen; Søren Vang; Lars Dyrskjøt; Thomas B Hansen; Jakob S Pedersen

doi:10.1093/narcan/zcad041

Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer

NAR Cancer. 2023 Aug 7;5(3):zcad041. doi: 10.1093/narcan/zcad041. eCollection 2023 Sep.

Authors

Asta M Rasmussen^{1

2

3}, Trine Line H Okholm⁴, Michael Knudsen^{1

2}, Søren Vang^{1

2}, Lars Dyrskjøt^{1

2}, Thomas B Hansen⁵, Jakob S Pedersen^{1

2

3}

Affiliations

¹ Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark.
² Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark.
³ Bioinformatics Research Center (BiRC), Aarhus University, Aarhus 8000, Denmark.
⁴ Departments of Otolaryngology-Head and Neck Surgery and Microbiology & Immunology, University of California, San Francisco, CA, USA.
⁵ Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus 8000, Denmark.

Abstract

Until recently, intronic lariats were regarded as short-lasting splicing byproducts with no apparent function; however, increasing evidence of stable derivatives suggests regulatory roles. Yet little is known about their characteristics, functions, distribution, and expression in healthy and tumor tissue. Here, we profiled and characterized circular stable intronic sequence RNAs (sisRNAs) using total RNA-Seq data from bladder cancer (BC; n = 457, UROMOL cohort), healthy tissue (n = 46), and fractionated cell lines (n = 5). We found that the recently-discovered full-length intronic circles and the stable lariats formed distinct subclasses, with a surprisingly high intronic circle fraction in BC (∼45%) compared to healthy tissues (0-20%). The stable lariats and their host introns were characterized by small transcript sizes, highly conserved BP regions, enriched BP motifs, and localization in multiple cell fractions. Additionally, circular sisRNAs showed tissue-specific expression patterns. We found nine circular sisRNAs as differentially expressed across early-stage BC patients with different prognoses, and sisHNRNPK expression correlated with progression-free survival. In conclusion, we identify distinguishing biological features of circular sisRNAs and point to specific candidates (incl. sisHNRNPK, sisWDR13 and sisMBNL1) that were highly expressed, had evolutionary conserved sequences, or had clinical correlations, which may facilitate future studies and further insights into their functional roles.