RNA editing is a finely tuned, dynamic mechanism for post-transcriptional gene regulation that has been thoroughly investigated in the last decade. In this work we analyse the variations in microRNA seed region editing activity during a time course of a hypoxia-exposed breast cancer cell line.

By leveraging on recent innovative bioinformatics approaches applied to a more informative experimental context, we have analysed small RNA-seq (sRNA-seq) data obtained from a hypoxia-treated breast cancer cell line over time, focusing specifically on miRNA post-transcriptional modifications occurring in the miRNA seed region (MSR), with particular attention to A-to-I editing events.

To estimate the impact of editing on miRNA function during hypoxia progression, we decided to investigate A-to-G miRNA modifications, as these are expected to be the result of A-to-I editing. Specifically, we decided to consider all A-to-I editing events occurring in MSRs (2-8 nt seed region). Subsequently, in order to compare the target sets of the wild type (WT) and edited (ED) versions of each miRNA, we performed binding site prediction on gene 3’-UTRs by multiple prediction tool consensus. Furthermore, our target prediction results were validated experimentally. Finally, employing gene microarray data associated to the sRNA-seq data, we performed differential gene expression analysis followed by functional enrichment, focusing on hypoxia-related pathways, such as VEGF and PI3K/Akt, to evaluate how the miRNA editing phenomenon could affect these pathways during the hypoxic time course.

We identified a total of 29 statistically significant canonical and non-canonical editing sites in 20 different miRNAs, with 8 sites previously known. The average modification levels of the majority of MSRs generally increased with time of exposure to hypoxia. We found that microRNA editing events in the seed region are not depended on microRNA expression. Additionally, the evidence that emerges from our functional data shows, indeed, how the editing of certain miRNAs is significantly associated with the cellular response to hypoxic stimulus, unprecedentedly providing insights on the meaning of the target set shift derived from these modifications. This reveals that microRNA editing acts under the influence of environmentally induced stimuli.

Our results, thus, show a microRNA editing activity trend in favour of cellular pathways closely associated to hypoxia, providing novel insights on the functional role of miRNA seed region editing. This provides a foundation for further elucidation of the miRNA editing phenomenon, giving a direction to future innovative investigation of its biological importance and potential involvement in physiological and pathological cellular changes.

Citation Format: Mario Acunzo, Giovanni Nigita, Giulia Romano, Dario Veneziano, Alessandro Lagana’, Dorothee Wernicke, Alfredo Ferro, Carlo Croce. miRNA editing in seed region is in synergy with cellular changes in hypoxic conditions. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-166.