An Integrative Meta-analysis of MicroRNAs in Hepatocellular Carcinoma

We aimed to shed new light on the roles of microRNAs (miRNAs) in liver cancer using an integrative in silico bioinformatics analysis. A new protocol for target prediction and functional analysis is presented and applied to the 26 highly differentially deregulated miRNAs in hepatocellular carcinoma....

Full description

Saved in:
Bibliographic Details
Published in:Genomics, proteomics & bioinformatics proteomics & bioinformatics, 2013-12, Vol.11 (6), p.354-367
Main Authors: ElHefnawi, Mahmoud, Soliman, Bangli, Abu-Shahba, Nourhan, Amer, Marwa
Format: Article
Language:English
Subjects:
bioinformatics
Cancer hallmarks
carcinogenesis
energy
genes
Hepatocellular carcinoma
hepatoma
homeostasis
Integrative bioinformatics
meiosis
meta-analysis
Meta分析
microarray technology
microRNA
miRNA
miRNAs
mitogen-activated protein kinase
oocytes
Original Research
prediction
prostatic neoplasms
stem cells
Target prediction
transforming growth factor beta
原发性肝癌
小分子RNA
整合
相互作用能
肿瘤抑制基因
预测工具
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:We aimed to shed new light on the roles of microRNAs (miRNAs) in liver cancer using an integrative in silico bioinformatics analysis. A new protocol for target prediction and functional analysis is presented and applied to the 26 highly differentially deregulated miRNAs in hepatocellular carcinoma. This framework comprises: (1) the overlap of prediction results by four out of five target prediction tools, including TargetScan, PicTar, miRanda, DIANA-microT and miRDB (combining machine-learning, alignment, interaction energy and statistical tests in order to minimize false positives), (2) evidence from previous microarray analysis on the expression of these targets, (3) gene ontology (GO) and pathway enrichment analysis of the miRNA targets and their pathways and (4) linking these results to oncogenesis and cancer hallmarks. This yielded new insights into the roles of miRNAs in cancer hallmarks. Here we presented several key targets and hundreds of new targets that are significantly enriched in many new cancer-related hallmarks. In addition, we also revealed some known and new oncogenic pathways for liver cancer. These included the famous MAPK, TGFβ and cell cycle pathways. New insights were also provided into Wnt signaling, prostate cancer, axon guidance and oocyte meiosis pathways. These signaling and developmental pathways crosstalk to regulate stem cell transformation and implicate a role of miRNAs in hepatic stem cell deregulation and cancer development. By analyzing their complete interactome, we proposed new categorization for some of these miRNAs as either tumor-suppressors or oncomiRs with dual roles. Therefore some of these miRNAs may be addressed as therapeutic targets or used as therapeutic agents. Such dual roles thus expand the view of miRNAs as active maintainers of cellular homeostasis.
ISSN:1672-0229
2210-3244
DOI:10.1016/j.gpb.2013.05.007