Bioinformatic Interrogation of 5p-arm and 3p-arm Specific miRNA Expression Using TCGA Datasets

MicroRNAs (miRNAs) play important roles in cellular functions and developmental processes. They are also implicated in oncogenesis mechanisms and could serve as potential cancer biomarkers. Using high-throughput miRNA sequencing information, expression of both the 5p-arm and 3p-arm mature miRNAs were demonstrated and generated from the single miRNA hairpin precursor. However, current miRNA annotations lack comprehensive 5p-arm/3p-arm feature annotations. Among known human mature miRNAs, only half of them are annotated with arm features. This generated ambiguous results in many miRNA-Sequencing (miRNA-Seq) studies. In this report, we have interrogated the TCGA (the Cancer Genome Atlas) miRNA expression datasets with an improved, fully annotated human 5p-arm and 3p-arm miRNA reference list. By utilizing this comprehensive miRNA arm-feature annotations, enhanced determinations and clear annotations were achieved for the miRNA isoforms (isomiRs) recognized from the sequencing reads. In the gastric cancer (STAD) dataset, as an example, 32 5p-arm/3p-arm OPEN ACCESS J. Clin. Med. 2015, 4 1799 specific miRNAs were found to be down-regulated and 24 5p-arm/3p-arm specific miRNAs were found to be up-regulated. We have further extended miRNA biomarker discoveries to additional TCGA miRNA-Seq datasets and provided extensive expression information on 5p-arm/3p-arm miRNAs across multiple cancer types. Our results identified several miRNAs that could be potential common biomarkers for human cancers.

Interrogation of microRNAs involved in gastric cancer using 5p-arm and 3p-arm annotated microRNAs

MicroRNAs are derived from endogenous stem-loop precursors, and play important roles in various biological processes. From next-generation sequencing data, it is suggested that both the 5p-arm and 3p-arm of mature miRNAs could be generated from a single miRNA hairpin precursor; however, the current miRNA databases fail to provide comprehensive arm annotation features, which could result in ambiguous and incomplete analyses. In the present report, we have annotated over 99.7% of miRNAs with the correct 5p-arm and 3p-arm features. The length distribution of all annotated miRNAs is around 22 nucleotides; however, the 5p-arm miRNAs seem to be longer than those of the 3p-arm, which is evident in the 23-nucleotide group. Our study effort generates comprehensive miRNA arm-feature annotation which can be utilized for better interrogation of miRNAs. In further analysis of human gastric cancer tissues, we identified 38 down-regulated miRNAs and 22 up-regulated arm-specific miRNAs using this new comprehensives miRNA list.