Pan-cancer characterisation of microRNA across cancer hallmarks reveals microRNA-mediated downregulation of tumour suppressors

• Published in: Nature communications 2018-12, Vol.9 (1), p.5228-13, Article 5228
• Main Authors: Dhawan, Andrew, Scott, Jacob G., Harris, Adrian L., Buffa, Francesca M.
• Format: Article
• Language: English
• Subjects: 38/91; 45/23; 45/61; 631/114/2164; 631/208/176/2016; 631/208/212/2019; 631/67/69; 692/4028/67/69; Aging; Biological activity; Cadherins - genetics; Cancer; Cell Proliferation - genetics; Copy number; Cyclin-Dependent Kinases - genetics; Down-Regulation; Epithelial-Mesenchymal Transition - genetics; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Gene regulation; Gene Regulatory Networks; Genomes; Humanities and Social Sciences; Humans; Membrane Proteins - genetics; Methylation; MicroRNAs; MicroRNAs - genetics; miRNA; multidisciplinary; Mutation; Neoplasms - classification; Neoplasms - genetics; PTEN Phosphohydrolase - genetics; PTEN protein; Redundancy; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Signal Transduction - genetics; Suppressors; Tumor suppressor genes; Tumor Suppressor Proteins - genetics; Tumors
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-07657-1

microRNAs are key regulators of the human transcriptome across a number of diverse biological processes, such as development, aging and cancer, where particular miRNAs have been identified as tumour suppressive and oncogenic. In this work, we elucidate, in a comprehensive manner, across 15 epithelial cancer types comprising 7316 clinical samples from the Cancer Genome Atlas, the association of miRNA expression and target regulation with the phenotypic hallmarks of cancer. Utilising penalised regression techniques to integrate transcriptomic, methylation and mutation data, we find evidence for a complex map of interactions underlying the relationship of miRNA regulation and the hallmarks of cancer. This highlighted high redundancy for the oncomiR-1 cluster of oncogenic miRNAs, in particular hsa-miR-17-5p. In addition, we reveal extensive miRNA regulation of tumour suppressor genes such as PTEN, FAT4 and CDK12, uncovering an alternative mechanism of repression in the absence of mutation, methylation or copy number changes. miRNAs have emerged as regulators of diverse biological processes including cancer. Here the authors present an extended pan-cancer analysis of the miRNAs in 15 epithelial cancers; integrating methylation, transcriptomic and mutation data they reveal alternative mechanisms of tumour suppressors’ regulation in absence of mutation, methylation or copy number alterations.