J Cancer 2019; 10(11):2552-2559. doi:10.7150/jca.28167

Research Paper

Identifying miRNA-mRNA Pairs and Novel miRNAs from Hepatocelluar Carcinoma miRNomes and TCGA Database

Ping Wu1*, Yunyue Xiao2*, Tao Guo1, Yitao Wang1, Shanshan Liao3, Lang Chen3✉, Zhisu Liu1✉

1. Department of Hepatobiliary and Pancreas, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P.R. China.
2. Institute of Digestive, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China.
3. Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, P.R. China.
* These authors contributed equally to this work.

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Citation:
Wu P, Xiao Y, Guo T, Wang Y, Liao S, Chen L, Liu Z. Identifying miRNA-mRNA Pairs and Novel miRNAs from Hepatocelluar Carcinoma miRNomes and TCGA Database. J Cancer 2019; 10(11):2552-2559. doi:10.7150/jca.28167. Available from http://www.jcancer.org/v10p2552.htm

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Abstract

Increasing evidence shows microRNAs (miRNAs) are engaged in hepatocelluar carcinoma (HCC). To identify novel feasible miRNA/mRNA pairs involved in hepatocarcinogenesis, an in-depth analysis of miRNomes in human non-tumor liver and HCC samples was carried out in this study. Firstly, differentially expressed miRNAs were obtained from deep sequencing of 15 liver samples, and verified in an independent data from The Cancer Genome Atlas (TCGA) database. Then, differentially expressed mRNA targets were selected from TCGA, and the differential miRNA/mRNA pairs with negative correlations were screened out. Finally, functional enrichment analysis was used to predict the functions of miRNA/mRNA pairs in HCC. In our study, 81 miRNA/mRNA pairs and 7 novel miRNAs were found. We constructed a hub interaction model with 9 miRNA/mRNA pairs to further investigate molecular mechanism of HCC. Survival analysis identified nine genes (hsa-miR-137, hsa-miR-490, BIRC5, TOP2A, CDC25C, IGF2BP1, IQGAP3, NCAPG and VIPR1) with significant influence on prognosis of HCC patients. In conclusion, the miRNA/mRNA pairs identified in our study may have some potential values to be further studied in progression, diagnosis and prognosis of HCC.