Abstract
Over the last 15 years, the several hundreds of identified microRNAs have been proposed to control numerous biological processes in healthy conditions or diseases. We studied two aspects of microRNA biology: the biological role of a perceived microRNA as a tumor suppressor; and the control of microRNA stability. Some microRNAs have been presented to act as pro-oncogenic or tumor-suppressor due to their role in controlling critical cellular pathways in the establishment of cancer. Nevertheless, a consensual definition of tumor-suppressing microRNAs is still missing. Similar to coding genes, we propose that tumor suppressor microRNAs must show evidence of genetic or epigenetic inactivation in cancers and exhibit an anti-proliferative activity under endogenous expression levels. In a first project, we tried out this definition with the miR-34a microRNA, which has attracted a lot of attention because it is regulated by the tumor-suppressor transcription factor p53 and became the first microRNA-based drug reaching clinical trial phase 1 in oncology. We used cancer genetics data to assess the expression level and the genetic status of miR-34a in multiple cancer types. We also performed genetic ablation to measure the endogenous function of this microRNA on cell proliferation in cancer cell lines and investigated in-depth previous over-expression studies showing its anti-proliferative effect to explain discrepancies with our results. Browsing a large diversity of cancer types, it appears that miR-34a is not down-regulated in primary tumors relative to normal adjacent tissues, and its gene does not accumulate mutations in cancer. Our work also shows that the established anti-proliferative action of miR-34a was based on over-expression experiments, leading to unrealistically high microRNA levels. Our data indicate that endogenous miR-34a levels do not have such an effect; therefore argue against a tumor-suppressive function for miR-34a.MicroRNAs repress mRNAs, but reciprocally, target mRNAs can also modulate microRNA stability. In a second project, we considered the endogenous regulation of microRNAs by mRNAs through target RNA-directed microRNA degradation (TDMD). Artificial targets as well as in vivo examples (viral transcripts, long non-coding RNAs libra in zebrafish and Cyrano in mouse) have shown that extensive complementarity between a target RNA and a microRNA triggers the proteolysis of the microRNA-Induced Silencing Complex by the ubiquitin-proteasome pathway, which exposes the microRNA for degradation. Based on published data about target RNA patterns leading to TDMD and phylogenetic conservation, we developed a computational tool for the in silico identification of RNA sites that induce microRNA degradation through TDMD. Supplemented with published RNA-seq and small-RNA-seq data, our software allows to focus on cell-specific TDMD inducer candidates. Our search uncovered several convincing candidates in mouse neurons and their molecular characterization has been initiated.