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

Journal of Clinical Medicine

Wei-Ting Kuo²  Ming-Wei Su²  Yungling Leo Lee²  Chien-Hsiun Chen²  Chew-Wun Wu¹  Wen-Liang Fang¹  Kuo-Hung Huang¹  Wen-chang Lin²  Takahiro Ochiya³ 

[1] Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei 112, Taiwan; E-Mails:;Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; E-Mails:Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan;

关键词: microRNA;    5p-arm;    3p-arm;    bioinformatics;    TCGA;    biomarker;   

DOI  :  10.3390/jcm4091798

来源: mdpi

【 摘 要 】

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 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.

【 授权许可】

CC BY   
© 2015 by the authors; licensee MDPI, Basel, Switzerland.