Poster Presentation 44th Lorne Genome Conference 2023

Systematic loss of function screens identify pathway specific functional circular RNAs (#273)

Matthew Neve 1 , Ling Liu 1 , Laura Perlaza-Jimenez 1 , Azelle Hawdon 1 , Simon Conn 2 , Jennifer Zenker 1 , Pablo Tomayo 3 , Greg Goodall 4 , Joseph Rosenbluh 1
  1. Monash University, Melbourne, Victoria, Australia
  2. Flinders University, Adelaide, South Australia, Australiua
  3. University of California, San Diego, San Diego, California
  4. Centre for Cancer Biology SA Pathology and University of South Australia, Adelaide, South Australia

Circular RNAs (circRNAs) are covalently closed single stranded RNAs that are produced by RNA back-splicing. A small number of circRNAs have been implicated as functional, however, we still lack systematic understanding of cellular processes and signalling pathways that are regulated by circRNAs. A major gap in understanding circRNA function is the ability to define pathways that are regulated by circRNAs. Here, we generated a pooled shRNA library targeting the back-splice junction of 3,354 human circRNAs that are expressed at low to high levels in humans. We used this library for loss of function proliferation screens in a panel of 18 cancer cell lines from four tissue types that harbour mutations leading to constitutive activity of defined pathways. Using this dataset, we identify context specific and non-specific circRNAs. We validated these observations with a secondary screen and uncovered a role for circRERE, a cell essential circRNA that regulates ferroptosis. Furthermore, we characterised the functional roles of pathway-specific circRNA, circSMAD2, a novel regulator of the WNT pathway and circMTO1, a regulator of MAPK signalling in a PTEN dependent manner. Our work sheds light on molecular pathways regulated by circRNAs and provides a catalogue of circRNAs with a measurable function in human cells.