Abonnement à la biblothèque: Guest
Critical Reviews™ in Eukaryotic Gene Expression

Publication de 6  numéros par an

ISSN Imprimer: 1045-4403

ISSN En ligne: 2162-6502

The Impact Factor measures the average number of citations received in a particular year by papers published in the journal during the two preceding years. 2017 Journal Citation Reports (Clarivate Analytics, 2018) IF: 1.6 To calculate the five year Impact Factor, citations are counted in 2017 to the previous five years and divided by the source items published in the previous five years. 2017 Journal Citation Reports (Clarivate Analytics, 2018) 5-Year IF: 2.2 The Immediacy Index is the average number of times an article is cited in the year it is published. The journal Immediacy Index indicates how quickly articles in a journal are cited. Immediacy Index: 0.3 The Eigenfactor score, developed by Jevin West and Carl Bergstrom at the University of Washington, is a rating of the total importance of a scientific journal. Journals are rated according to the number of incoming citations, with citations from highly ranked journals weighted to make a larger contribution to the eigenfactor than those from poorly ranked journals. Eigenfactor: 0.00058 The Journal Citation Indicator (JCI) is a single measurement of the field-normalized citation impact of journals in the Web of Science Core Collection across disciplines. The key words here are that the metric is normalized and cross-disciplinary. JCI: 0.33 SJR: 0.345 SNIP: 0.46 CiteScore™:: 2.5 H-Index: 67

Indexed in

Reconstruction and Analysis of the Differentially Expressed IncRNA-miRNA-mRNA Network Based on Competitive Endogenous RNA in Hepatocellular Carcinoma

Volume 29, Numéro 6, 2019, pp. 539-549
DOI: 10.1615/CritRevEukaryotGeneExpr.2019028740
Get accessGet access

RÉSUMÉ

Hepatocellular carcinoma (HCC) is a common and aggressive malignant neoplasm with an increasing incidence rate among cancers worldwide. This study aimed to establish a competing-endogenous RNA (ceRNA) network to further understand the ceRNA regulatory mechanism and pathogenesis in HCC. mRNA and miRNA expression data and corresponding clinical characteristics of HCC patients were downloaded from The Cancer Genome Atlas Data Portal. The different expression profiles of mRNA, lncRNA, and miRNA (referred to as DEmRNAs, DElncRNAs, and DEmiR-NAs, respectively) screened 374 HCC tumor tissues and 50 adjacent nontumor control tissues. The miRcode database was used to predict interactions between DElncRNAs and DEmiRNAs. The miRTarBase, miRDB, and TargetScan databases were used to retrieve miRNA-targeted mRNAs. The lncRNA-miRNA-mRNA ceRNA network was constructed based on matched DElncRNA-DEmiRNA and DEmiRNA-DEmRNA pairs. Functional enrichment analysis revealed the biological processes and pathways of DEmRNAs involved in the development of HCC. Key differentially expressed RNAs in the ceRNA network were further analyzed for their relationships with overall survival in HCC patients. A total of 1,982 mRNAs, 1,081 lncRNAs, and 126 miRNAs were identified as differentially expressed. The ceRNA network was constructed including 74 DElncRNAs, 35 DEmRNAs, and 16 DEmiRNAs. 13 DElncRNAs and 19 DEmRNAs were identified as prognosis-related biomarkers. Twenty-five Gene Ontology terms and 8 Kyoto Encyclopedia of Genes and Genomes pathways were found to be significantly enriched by DEmRNAs in the ceRNA network. Our results demonstrated tumor-specific mRNA, lncRNA, and miRNA expression patterns and enabled us to construct a ceRNA network that provided new insights into the molecular mechanisms of HCC. Key differentially expressed RNAs associated with total survival were also identified as promising biomarkers for survival prediction.

RÉFÉRENCES
  1. Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A. Global cancer statistics, 2012. Cancer J Clin. 2015;65(2):87-108.

  2. Bodzin AS, Busuttil RW. Hepatocellular carcinoma: advances in diagnosis, management, and long-term outcome. World J Hepatol. 2015;7(9):1157-67.

  3. Maluccio M, Covey A. Recent progress in understanding, diagnosing, and treating hepatocellular carcinoma. Cancer J Clin. 2012;62(6):394-9.

  4. Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nature Rev Gen. 2014;15(1):7-21.

  5. Dhamija S, Diederichs S. From junk to master regulators of invasion: lncRNA functions in migration, EMT and metastasis. Int J Cancer. 2016;139(2):269-80.

  6. Chi HC, Tsai CY, Tsai MM, Yeh CT, Lin KH. Roles of long noncoding RNAs in recurrence and metastasis of radiotherapy-resistant cancer stem cells. Int J Mol Sci. 2017;18(9):1903.

  7. Xie CR, Wang F, Zhang S, Wang FQ, Zheng S, Li Z. Long noncoding RNA HCAL facilitates the growth and metastasis of hepatocellular carcinoma by acting as a ceRNA of LAPTM4B. Molecular therapy. Nucleic Acids. 2017;9:440-51.

  8. Song J, Ye A, Jiang E, Yin X, Chen Z, Bai G. Reconstruction and analysis of the aberrant lncRNA-miRNA-mRNA network based on competitive endogenous RNA in CESC. J Cell Biochem. 2018 Aug;119(8):6665-73.

  9. Fang XN, Yin M, Li H, Liang C, Xu C, Yang GW, Zhang HX. Comprehensive analysis of competitive endogenous RNA network associated with head and neck squamous cell carcinoma. Sci Rep. 2018 Jul 12;8(1):10544.

  10. Xu S, Sui J, Yang S, Liu Y, Wang Y, Liang G. Integrative analysis of competing endogenous RNA network focusing on long noncoding RNA associated with progression of cutaneous melanoma. Cancer Med. 2018 Apr;7(4):1019-29.

  11. Fan Q, Liu B. Comprehensive analysis of a long noncoding RNA-associated competing endogenous RNA network in colorectal cancer. OncoTargets Ther. 2018;11:2453-66.

  12. Huang X, Xiao R, Pan S, Yang X, Yuan W, Tu Z. Uncovering the roles of long non-coding RNAs in cancer stem cells. J Hematol Oncol. 2017;10(1):62.

  13. Gomes AQ, Nolasco S, Soares H. Non-coding RNAs: multi-tasking molecules in the cell. Int J Mol Sci. 2013;14(8):16010-39.

  14. Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the rosetta stone of a hidden RNA language? Cell. 2011;146(3):353-8.

  15. Cao C, Zhang T, Zhang D, Xie L, Zou X, Lei L, Wu D, Liu L. The long non-coding RNA, SNHG6-003, functions as a competing endogenous RNA to promote the progression of hepatocellular carcinoma. Oncogene. 2017 Feb 23;36(8):1112.

  16. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-40.

  17. Ashwini J, Marks DS, Erik L. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics. 2012;28(15):2062.

  18. Chou CH, Chang NW, Shrestha S, Hsu SD, Lin YL, Lee WH, Yang CD, Hong HC, Wei TY, Tu SJ, Tsai TR, Ho SY, Jian TY, Wu HY, Chen PR, Lin NC, Huang HT, Yang TL, Pai CY, Tai CS, Chen WL, Huang CY, Liu CC, Weng SL, Liao KW, Hsu WL, Huang HD. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res. 2016;44(Database issue):D239.

  19. Wong N, Wang X. miRDB: an online resource for mi-croRNA target prediction and functional annotations. Nucleic Acids Res. 2015;43(Database issue):D146-152.

  20. Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. A uniform system for the annotation of vertebrate microRNA genes and the evolution of the human microRNAome. Annu Rev Gen. 2015;49(1):213-42.

  21. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498.

  22. Qin C, Han Z, Qian J, Bao M, Li P, Ju X, Zhang S, Zhang L, Li S, Cao Q, Lu Q. Expression pattern of long non-coding RNAs in renal cell carcinoma revealed by microarray. PLoS One. 2014;9(6):e99372.

  23. Serghiou S, Kyriakopoulou A, Ioannidis JPA. Long non-coding RNAs as novel predictors of survival in human cancer: a systematic review and meta-analysis. Mol Cancer. 2016;15(1):1-14.

  24. Lv J, Fan HX, Zhao XP, Bao M, Li P, Ju X, Zhang S, Zhang L, Li S, Cao Q, Lu Q, Li J, Shao P, Meng X, Zhang W, Yin C. Long non-coding RNA unigene 56159 promotes epithelial-mesenchymal transition by acting as a ceRNA of miR-140-5p in hepatocellular carcinoma cells. Cancer Lett. 2016;382(2):166-75.

  25. Yue B, Cai D, Liu C, Fang C, Yan D. Linc00152 functions as a competing endogenous RNA to confer oxaliplatin resistance and holds prognostic values in colon cancer. Mol Ther. 2016;24(12):2064-77.

  26. CY, Liang GY, Yao WZ, Sui J, Shen X, Zhang YQ, Peng H, Hong WW, Ye YC, Zhang ZY, Zhang WH, Yin LH, Pu YP. Integrated analysis of long non-coding RNA competing interactions reveals the potential role in progression of human gastric cancer. Int J Oncol. 2016;48(5):1965-76.

  27. Liu D, Yu X, Wang S, Dai E, Jiang L, Wang J, Yang Q, Yang F, Zhou S, Jiang W. The gain and loss of long non-coding RNA associated-competing endogenous RNAs in prostate cancer. Oncotarget. 2016;7(35):57228-38.

  28. Shuang Y, Ning Q, Zhang G, Hong S, Zhen W, Li Y. Construction of differential mRNA-lncRNA crosstalk networks based on ceRNA hypothesis uncover key roles of lncRNAs implicated in esophageal squamous cell carcinoma. Oncotarget. 2016;7(52):85728.

  29. Wang Q, Zhang J, Liu Y, Zhang W, Zhou J, Duan R, Pu P, Kang C, Han L. A novel cell cycle-associated lncRNA, HOXA11-AS, is transcribed from the 5-prime end of the HOXA transcript and is a biomarker of progression in glioma. Cancer Lett. 2016;373(2):251-9.

  30. Sun Y, Zhou Y, Bai Y, Wang Q, Bao J, Luo Y, Guo Y, Guo L. A long non-coding RNA HOTTIP expression is associated with disease progression and predicts outcome in small cell lung cancer patients. Mol Cancer. 2017;16(1):162.

  31. Lai Y, Xu P, Liu J, Li Q, Ren D, Zhang J, Wang J. Decreased expression of the long non-coding RNA MLLT4 antisense RNA 1 is a potential biomarker and an indicator of a poor prognosis for gastric cancer. Oncol Lett. 2017;14(3):2629.

  32. Zhang JH, Li AY, Wei N. Downregulation of long non-coding RNA LINC01133 is predictive of poor prognosis in colorectal cancer patients. Eur Rev Med Pharmacol Sci. 2017:2103-7.

  33. Gonzalez D, Else M, Wren D, Usai M, Buhl AM, Parker A, Oscier D, Morgan G, Catovsky D. CLLU1 expression has prognostic value in chronic lymphocytic leukemia after first-line therapy in younger patients and in those with mutated IGHV genes. Haematologica. 2013;98(2):274.

  34. Li YC, Wang D, Zhu GY. Increased expression of long noncoding RNA AK021443 predicts worse clinical outcome in hepatocellular carcinoma. Eur Rev Med Pharmacol Sci. 2018;22(15):4855-60.

  35. Zhang W, Qian S, Yang G, Zhu L, Zhou B, Wang J, Liu R, Yan Z, Qu X. MicroRNA-199 suppresses cell proliferation, migration and invasion by downregulating RGS17 in hepatocellular carcinoma. Gene. 2018;659:22-8.

  36. Pan XP, Huang LH, Wang X. MiR-370 functions as prog-nostic marker in patients with hepatocellular carcinoma. Eur Rev Med Pharmacol Sci. 2017;21(16):3581.

  37. Shi W, Zhang Z, Yang B, Guo H, Jing L, Liu T, Luo Y, Liu H, Li Y, Gao Y. Overexpression of microRNA let-7 correlates with disease progression and poor prognosis in hepatocellular carcinoma. Medicine (Baltimore, MD). 2017;96(32):e7764.

CITÉ PAR
  1. Xiong Yuanpeng, Ouyang Yonghao, Fang Kang, Sun Gen, Tu Shuju, Xin Wanpeng, Wei Yongyang, Xiao Weidong, Hussein Ahmed Faeq, Prediction of Prognosis and Molecular Mechanism of Ferroptosis in Hepatocellular Carcinoma Based on Bioinformatics Methods, Computational and Mathematical Methods in Medicine, 2022, 2022. Crossref

  2. Liu Huanqing, Li Tingting, Dong Chunsheng, Lyu Jun, Irshad Khushboo, Identification of miRNA signature for predicting the prognostic biomarker of squamous cell lung carcinoma, PLOS ONE, 17, 3, 2022. Crossref

Portail numérique Bibliothèque numérique eBooks Revues Références et comptes rendus Collections Prix et politiques d'abonnement Begell House Contactez-nous Language English 中文 Русский Português German French Spain