The role of RNA-RNA interactions in the post-transcriptional control of cancer-related genes: the case of circHIPK3/BRCA1 mRNA pairing

Circular RNAs are covalently-closed RNA molecules involved in gene-expression regulation at different levels. These peculiar molecules have recently attracted the attention of the scientific community especially due to their deregulation in different pathological conditions and recent technologies advances have allowed to better define their role in the cell. The work I carried out during my PhD aimed at elucidating the molecular mechanism through which the circular RNA circHIPK3, which results deregulated in different tumoral contexts, can influence cancer progression. While many studies describe circHIPK3 as a sponge of miRNAs, we looked for possible direct interactions with ubiquitously expressed mRNAs which could represent functional mechanisms conserved in different cancer types, regardless to specific miRNA signatures. We showed that circHIPK3 regulates the levels of BRCA1 protein, an essential DNA-repair factor, through a direct interaction between the circRNA back-splicing-junction (BSJ) and the last coding exon of BRCA1 mRNA. This interaction prevents the binding on the BRCA1 transcript of FMRP protein, which we identified as a BRCA1 translational repressor. We discovered this competitive model at first in embryonal rhabdomyosarcoma cell line (RD), we validated it in other tumoral contexts and we modulated it in different conditions to study phenotypic effects and possible therapeutic applications. We demonstrated that the disruption of circHIPK3/BRCA1 interaction causes BRCA1 protein down-regulation and consequent DNA-damage accumulation, strengthening the effects of DNA damage-inducing drugs and sensitizing BRCA1 wild-type tumour cells to PARP inhibitors by synthetic lethality. On the other hand, the inhibition of FMRP/BRCA1 interaction with locked-nucleic acids restores physiological BRCA1 levels and prevents DNA-damage accumulation in BRCA1 hemizygous breast cancer cells.