title: The RNA expression signature of the HepG2 cell line as determined by the integrated analysis of miRNA and mRNA expression profiles.
abstract: Understanding miRNAs' regulatory networks and target genes could facilitate the development of therapies for human diseases such as cancer. Although much useful gene expression profiling data for tumor cell lines is available, microarray data for miRNAs and mRNAs in the human HepG2 cell line have only been compared with that of other cell lines separately. The relationship between miRNAs and mRNAs in integrated expression profiles for HepG2 cells is still unknown. To explore the miRNA-mRNA correlations in hepatocellular carcinoma (HCC) cells, we performed miRNA and mRNA expression profiling in HepG2 cells and normal liver HL-7702 cells at the genome scale using next-generation sequencing technology. We identified 193 miRNAs that are differentially expressed in these two cell lines. Of these, 89 miRNAs were down-regulated in HepG2 cells compared with HL-7702 cells, while 104 miRNAs were up-regulated. We also observed 3035 mRNAs that are significantly dys-regulated in HepG2 cells. We then performed an integrated analysis of the expression data for differentially expressed miRNAs and mRNAs and found several miRNA-mRNA pairs that are significantly correlated in HepG2 cells. Further analysis suggested that these differentially expressed genes were enriched in four tumorigenesis-related signaling pathways, namely, ErbB, JAK-STAT, mTOR, and WNT, which until now had not been fully reported. Our results could be helpful in understanding the mechanisms of HCC occurrence and development.
authors.affiliation: School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China. Electronic address: whitecf@seu.edu.cn.
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Bai
authors.affiliation: School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Research Center for Learning Science, Southeast University, Nanjing 210096, China.
authors.forename: Xueying
authors.initials: X
authors.lastname: Xie
authors.affiliation: Nanjing Decode Genomics Biotechnology Co., Ltd., Nanjing 210019, China.
authors.forename: Tong
authors.initials: T
authors.lastname: Yu
authors.affiliation: School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China; College of Information Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Yihua
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Research Center for Learning Science, Southeast University, Nanjing 210096, China.
authors.forename: Qinyu
authors.initials: Q
authors.lastname: Ge
authors.affiliation: School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China; Research Center for Learning Science, Southeast University, Nanjing 210096, China. Electronic address: zhlu@seu.edu.cn.
authors.forename: Zuhong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D015536:Down-Regulation; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D056945:Hep G2 Cells; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000235:genetics; D015854:Up-Regulation
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger
keywords: HepG2/HL-7702; Integrative analysis; RNA expression; miRNA/mRNA