中文English
ISSN 1001-5256 (Print)
ISSN 2097-3497 (Online)
CN 22-1108/R
Volume 35 Issue 8
Aug.  2019
Turn off MathJax
Article Contents

Construction and functional enrichment analysis of circRNA-miRNA-mRNA regulatory network for liver cancer based on high-throughput sequencing

DOI: 10.3969/j.issn.1001-5256.2019.08.018
Research funding:

 

  • Received Date: 2019-03-15
  • Published Date: 2019-08-20
  • Objective To construct a protein interaction network based on high-throughput sequencing data of liver cancer-related non-coding RNAs, to perform a functional enrichment analysis, and to screen out circular RNAs (circRNAs) participating in the development and progression of liver cancer via the mechanism of competitive endogenous RNA (ceRNA) . Methods The circRNA-miRNA-mRNA network was constructed using gene expression omnibus (GEO) data based on the ceRNA theory. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analyses were performed to identify circRNAs with potential ceRNA function and explore their functions. Results A total of 9 co-expressed circRNAs, 20 co-expressed miRNAs, and 153 co-expressed mRNAs were screened out from the GEO database, and the liver cancer-related circRNA-miRNA-mRNA network was successfully constructed. The GO analysis revealed 90 biological processes, which mainly involved 12 functional clusters including hepatocyte differentiation, phase-change regulation of cell cycle, and negative regulation of transcription factor activity. The KEGG analysis showed that the co-expressed circRNAs were also involved in the p53 and PI3 K-Akt signaling pathways. Conclusion This study provides new insights for circRNAs mediating the development and progression of liver cancer through the mechanism of ceRNA.

     

  • loading
  • [1] EL-SERAG HB, RUDOLPH KL. Hepatocellular carcinoma:Epidemiology and molecular carcinogenesis[J]. Gastroenterology, 2007, 132 (7) :2557-2576.
    [2] LLOVET JM, MONTAL R, SIA D, et al. Molecular therapies and precision medicine for hepatocellular carcinoma[J]. Nat Rev Clin Oncol, 2018, 15 (10) :599-616.
    [3] SOLE C, ARNAIZ E, MANTEROLA L, et al. The circulating transcriptome as a source of cancer liquid biopsy biomarkers[J]. Semin Cancer Biol, 2019.[Epub ahead of print]
    [4] ZHONG Y, DU Y, XUE Y, et al. Circular RNAs function as ceRNAs to regulate and control human cancer progression[J]. Mol Cancer, 2018, 17 (1) :79.
    [5] YAO R, ZOU H, LIAO W. Prospect of circular RNA in hepatocellular carcinoma:A novel potential biomarker and therapeutic target[J]. Front Oncol, 2018, 8:332.
    [6] DONG Y, ZHANG X, XIE M, et al. Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication[J]. BMC Genomics, 2015, 16:431.
    [7] ZHOU M, WANG X, SHI H, et al. Characterization of long non-coding RNA-associated ceRNA network to reveal potential prognostic lncRNA biomarkers in human ovarian cancer[J].Oncotarget, 2016, 7 (11) :12598-12611.
    [8] WANG H, NIU L, JIANG S, et al. Comprehensive analysis of aberrantly expressed profiles of lncRNAs and miRNAs with associated ceRNA network in muscle-invasive bladder cancer[J]. Oncotarget, 2016, 7 (52) :86174-86185.
    [9] TREIBER T, TREIBER N, MEISTER G. Regulation of microRNA biogenesis and its crosstalk with other cellular pathways[J].Nat Rev Mol Cell Biol, 2019, 20 (1) :5-20.
    [10] SU Q, KUMAR V, SUD N, et al. MicroRNAs in the pathogenesis and treatment of progressive liver injury in NAFLD and liver fibrosis[J]. Adv Drug Deliv Rev, 2018, 129:54-63.
    [11] ZHOU W, YANG WL, ZHANG HW, et al. Advances in the relationship between microRNA-483 and digestive system tumors[J]. Chin J Dig Surg, 2018, 17 (5) :522-526. (in Chinese) 周威, 杨万里, 张洪伟, 等.微RNA-483与消化系统肿瘤关系的研究进展[J].中华消化外科杂志, 2018, 17 (5) :522-526.
    [12] LING H, FABBRI M, CALIN GA. MicroRNAs and other noncoding RNAs as targets for anticancer drug development[J].Nat Rev Drug Discov, 2013, 12 (11) :847-865.
    [13] WONG CM, TSANG FH, NG IO. Non-coding RNAs in hepatocellular carcinoma:Molecular functions and pathological implications[J]. Nat Rev Gastroenterol Hepatol, 2018, 15 (3) :137-151.
    [14] SU H, TAO T, YANG Z, et al. Circular RNA cTFRC acts as the sponge of MicroRNA-107 to promote bladder carcinoma progression[J]. Mol Cancer, 2019, 18 (1) :27.
    [15] ZHANG X, WANG S, WANG H, et al. Circular RNA circNRIP1acts as a microRNA-149-5p sponge to promote gastric cancer progression via the AKT1/m TOR pathway[J]. Molecular cancer, 2019, 18 (1) :20.
    [16] CAI M, XU L, SHEN L, et al. Expression of long-chain noncoding RNA FOXN3-AS2 in hepatocellular carcinoma and its effect on proliferation and invasion of hepatoma cells[J]. Chin J Clin Pharmacol Ther, 2018, 23 (11) :1246-1251. (in Chinese) 蔡民, 许浏, 沈兰, 等.长链非编码RNA FOXN3-AS2在肝癌中的表达及其对肝癌细胞增殖和侵袭的影响[J].中国临床药理学与治疗学, 2018, 23 (11) :1246-1251.
    [17] ZHANG X, XU Y, QIAN Z, et al. CircRNA_104075 stimulates YAP-dependent tumorigenesis through the regulation of HNF4a and may serve as a diagnostic marker in hepatocellular carcinoma[J]. Cell Death Dis, 2018, 9 (11) :1091.
    [18] BAI N, PENG E, QIU X, et al. CircFBLIM1 act as a ceRNA to promote hepatocellular cancer progression by sponging miR-346[J]. J Exp Clin Cancer Res, 2018, 37 (1) :172.
    [19] CHENG Q, NING D, CHEN J, et al. SIX1 and DACH1 influence the proliferation and apoptosis of hepatocellular carcinoma through regulating p53[J]. Cancer Biol Ther, 2018, 19 (5) :381-390.
    [20] CHEN JS, WANG Q, FU XH, et al. Involvement of PI3K/PTEN/AKT/m TOR pathway in invasion and metastasis in hepatocellular carcinoma:Association with MMP-9[J]. Hepatol Res, 2010, 39 (2) :177-186.
    [21] LIU D, CUI L, WANG Y, et al. Hepatitis B e antigen and its precursors promote the progress of hepatocellular carcinoma by interacting with NUMB and decreasing p53 activity[J].Hepatology, 2016, 64 (2) :390-404.
    [22] ZHANG ZY, HONG D, NAM SH, et al. SIRT1 regulates oncogenesis via a mutant p53-dependent pathway in hepatocellular carcinoma[J]. J Hepatol, 2015, 62 (1) :121-130.
    [23] HUANG Q, LI J, XING J, et al. CD147 promotes reprogramming of glucose metabolism and cell proliferation in HCC cells by inhibiting the p53-dependent signaling pathway[J]. J Hepatol, 2014, 61 (4) :859-866.
    [24] ZUO X, CHEN Z, CAI J, et al. 5-hydroxytryptamine receptor1D aggravates hepatocellular carcinoma progression through FoxO6 in AKT-dependent and independent manners[J].Hepatology, 2019, 69 (5) :2031-2047.
    [25] CHEN Z, GAO W, PU L, et al. PRDM8 exhibits antitumor activities toward hepatocellular carcinoma by targeting NAP1L1[J]. Hepatology, 2018.[Epub ahead of print]
    [26] LIU S, DU Y, MA H, et al. Preclinical comparison of regorafenib and sorafenib efficacy for hepatocellular carcinoma using multimodality molecular imaging[J]. Cancer Lett, 2019, 453:74-83.
    [27] DENG H, SHANG W, LU G, et al. Targeted and multifunctional technology for identification between hepatocellular carcinoma and liver cirrhosis[J]. ACS Appl Mater Interfaces, 2019, 11 (16) :14526-14537.
    [28] FAN YQ, DONG SL. Recent advances in targeted drug therapy for hepatocellular carcinoma[J]. J Clin Hepatol, 2018, 34 (2) :424-428. (in Chinese) 樊永强, 董胜利.靶向药物治疗肝细胞癌的最新进展[J].临床肝胆病杂志, 2018, 34 (2) :424-428.
    [29] LIU Y, FENG J, SUN M, et al. Long noncoding RNA HULC activates HBV by modulating HBx/STAT3/miR-539/APOBEC3B signaling in HBV-related hepatocellular carcinoma[J]. Cancer letters, 2019, 454:158-170.
    [30] MUKHERJI S, EBERT MS, ZHENG GX, et al. MicroRNAs can generate thresholds in target gene expression[J]. Nat Genet, 2011, 43 (9) :854-859.
    [31] WEE LM, FLORES-JASSO CF, SALOMON WE, et al. Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties[J]. Cell, 2012, 151 (5) :1055-1067.
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Article Metrics

    Article views (480) PDF downloads(755) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return