Abstract 232: Characterization of the human miRNA-ome reveals numerous novel, tissue-specific miRNAs that are implicated in cancer biology
Authors: Eric R. Londin, Phillipe D. Loher, Isidore Rigoutsos
Journal: Cancer Research (2015)

Abstract Background: MicroRNAs (miRNAs) are short, ∼22 nt RNAs that are important post-transcriptional regulators of transcript abundance. Since their initial discovery they have been shown to be involved in many cellular processes and their dysregulation has been associated with disease etiology including many cancers. Currently, nearly 2,500 human miRNAs are annotated in public repositories. Key questions in miRNA research include: how many miRNAs are expressed in the human genome? What are their functional roles in various cancers? Herein, we sought to examine the first question through the examination of short RNA-sequence datasets. Methods: We analyzed 1,323 short RNA sequencing datasets (RNA-seq) generated from normal and disease samples representing 13 different human tissue types. We applied the miRDeep2 algorithm on each sample to identify short transcripts that are significantly expressed within the sample that are predicted to form hairpin-shaped secondary structures. Results: Using miRDeep2 with stringent thresholding criteria we discovered 3,707 statistically significant novel mature miRNAs at a false discovery rate of ≤ 0.05 that arise from 3,494 precursor loci: 91.5% of these novel miRNAs were discovered independently in 10 or more of the RNA-seq datasets. Analysis of the newly discovered miRNAs reveals that they are tissue-specific in nature. Furthermore, analysis of HITS-CLIP data independently obtained from four of the 13 tissues reveals that 45% of the novel miRNAs are loaded on Argonaute an indication that these miRNAs are active in the RNA interference pathway. Sequence conservation analysis across vertebrate and invertebrate organisms revealed that 56.7% of these new miRNAs are human-specific and the majority of them (94.4%) are primate-lineage specific. Importantly, our profiling of the newly discovered miRNAs showed their differential abundance across different tumor types, and between normal and tumor, and allowed tumor classification. Using orthogonal experimental techniques we have also been able to independently validate several dozen of the novel miRNAs. Conclusions: By analyzing samples from 13 human tissues we discovered 3,707 new miRNAs. This suggests that the repertoire of human miRNAs is larger and more diverse than might have been surmised by the publicly available data. We emphasize that the novel miRNAs we discovered are primate-specific and tissue-specific. This indicates the existence of molecular interactions that cannot be recapitulated by mouse models. As these interactions are numerous and currently uncharacterized they have consequential implications for both the clinical and basic research of cancers. Additionally, the fact that the abundance of our novel miRNAs can distinguish among different tumor types has direct implications for cancer biology and suggests possible uses of these novel molecules for therapeutic and diagnostic purposes. Citation Format: Eric R. Londin, Phillipe D. Loher, Isidore Rigoutsos. Characterization of the human miRNA-ome reveals numerous novel, tissue-specific miRNAs that are implicated in cancer biology. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 232. doi:10.1158/1538-7445.AM2015-232