Discovery of novel circular RNAs of the apoptosis-related BAX gene in breast cancer, by combining nanopore and next-generation sequencing

Circular RNAs (circRNAs) have emerged as significant regulators of cancer biology. However, the characterization and the regulatory potential of circRNAs deriving from key apoptotic genes remain poorly understood in breast cancer. We aimed to comprehensively characterize circRNAs originating from the pro-apoptotic BAX gene and predict their regulatory potential in BC signaling. Targeted amplification of circular BAX transcripts was conducted in eleven cancerous and one non-cancerous breast cell lines, followed by third-generation (nanopore) and next-generation sequencing. Finally, extensive bioinformatic analysis was conducted. Therefore, we identified 106 circRNAs, 82 of which were novel. These circRNAs exhibited diverse biogenesis features, including exon skipping, intron retention, and rare inclusion of exon 5. Expression profiling revealed subtype-specific patterns, with several circRNAs being detected only in triple-negative or luminal BC subtypes, while circ-BAX-55b was detected exclusively in the non-cancerous cell line. Many circRNAs were predicted to sponge miRNAs such as miR-152-5p, miR-4802-5p, and miR-3619-5p, potentially modulating signaling pathways including MAPK, PI3K/AKT, and NFκB. Extensive sponging of miR-152-5p, which targets BAX mRNA, suggests a feedback mechanism modulating apoptosis. Several circRNAs also contain binding sites for RNA-binding proteins (RBPs) such as RBM6 and HNRNPF, possibly dictating RNA fate. Overlapping miRNA and RBP-binding sites imply complex competitive or cooperative interactions. Additionally, multiple circRNAs, such as circ-BAX-6c, displayed translation-related features. In conclusion, these findings reveal a novel repertoire of BAX circRNAs with putative roles in BC signaling and apoptosis regulation. Moreover, they constitute a valuable resource for functional studies as well as potential biomarkers or therapeutic targets in breastcancer.