Résumé
Circular RNAs (circRNAs) are regulatory RNA molecules influencing cancer onset and progression. In this study, we used nanopore sequencing for circRNA profiling in multiple myeloma (MM). Total RNA extracts from 10 MM cell lines were subjected to rRNA depletion, RNase R treatment, and rolling-circle reverse transcription. Next, nanopore sequencing was conducted using the PromethION 2 Solo platform. Data were analyzed using CIRI-long 1.1.0 and in-house-developed algorithms. Thus, the circRNA-enriched fractions yielded 94 048 full-length circRNA sequences. Interestingly, these circRNAs are produced from 14 313 genes, indicating complex alternative splicing patterns, including the presence of novel exons and intron retention. Exemplary cases are CCND1, a target of t(11;14) translocation, which yields 18 circRNAs, NSD2, affected by t(4;14) translocation, producing 36 circRNAs, and BRAF, being transcribed into 49 circRNAs. In addition, many identified circRNAs are clustered in chromosomal hotspots for MM, such as chr11q13.1, chr16q22.1, and chr9q34.11. Notably, enrichment analysis of gene sets from the Molecular Signatures Database showed that many parental genes are involved in cell cycle regulation and are upregulated during unfolded protein response or through the activation of mTORC1 complex, all hallmarks of MM pathogenesis. Moreover, a great heterogeneity was observed between cell lines; 63,4% of the identified circRNAs were expressed in 1 cell line only, whereas 149 circRNAs were found in all 10 cell lines. Of note, pathway analysis revealed that 103 out of 149 circRNAs are produced from genes implicated in mitophagy, highlighting a pivotal process in the development and drug sensitivity of MM. In conclusion, we successfully characterized the wide diversity of the circular transcriptome in MM, laying a foundation for studying its role in MM pathogenesis. Acknowledgement: Funded by the EU Horizon Europe research and innovation programme (Project 101097094 – ELMUMY).