GSE168566
Target Directed miRNA degradation is pervasive in human cancer
How many RNA transcripts can induce degradation of microRNAs (miRNA) via the mechanism known as target-directed miRNA degradation (TDMD) is currently unknown. We developed TDMDfinder, a bioinformatics pipeline and webtool, which is based on combined sequence alignment and feature selection approaches to identify 'high confidence' TDMD interactions either in Human or Mouse transcriptomes. Predictions suggest that TDMD is widespread, and every miRNA is possibly under the control of endogenous targets. Experimental validations support the validity of TDMDfinder predictions with 49% accuracy, revealing novel endogenous TDMDs for miR-17, miR-19, miR-30, miR-221, miR-26 and miR-23 families. TDMD can selectively target specific miRNA family/cluster members. Features like complementarity to the miRNA 3' region, bulge size and hybridization energy can explain the different sensitivity. A set of computational analyses performed using the multiomic TCGA platform support the involvement of TDMD in human cancer. Many TDMD transcripts showed significant anti-correlations with both miRNA levels and miRNA activity in multiple tumors and 36 highly significant Pan-cancer interactions were highlighted. A proof-of-principle TDMD-pair was experimentally dissected in breast cancer, showing that fully-functioning TDMD could impact on cancer phenotypes, such as mammosphere growth and resistance to drug treatment. Our tool unveils TDMD as a widespread mechanism and pinpoints it as new potential oncogenic mechanism. Overall design: Examination of miRNA levels  upon over-expression of putative microRNA degradation elements (MDEs). Analysis should be conducted considering paired samples (i.e. those indicated with the same Experiment_number).