title: Integrated analysis of microRNA regulatory network in nasopharyngeal carcinoma with deep sequencing.
abstract: BACKGROUND
  MicroRNAs (miRNAs) have been shown to play a critical role in the development and progression of nasopharyngeal carcinoma (NPC). Although accumulating studies have been performed on the molecular mechanisms of NPC, the miRNA regulatory networks in cancer progression remain largely unknown. Laser capture microdissection (LCM) and deep sequencing are powerful tools that can help us to detect the integrated view of miRNA-target network.
  
  
  METHODS
  Illumina Hiseq2000 deep sequencing was used to screen differentially expressed miRNAs in laser-microdessected biopsies between 12 NPC and 8 chronic nasopharyngitis patients. The result was validated by real-time PCR on 201 NPC and 25 chronic nasopharyngitis patients. The potential candidate target genes of the miRNAs were predicted using published target prediction softwares (RNAhybrid, TargetScan, Miranda, PITA), and the overlay part was analyzed in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological process. The miRNA regulatory network analysis was performed using the Ingenuity Pathway Analysis (IPA) software.
  
  
  RESULTS
  Eight differentially expressed miRNAs were identified between NPC and chronic nasopharyngitis patients by deep sequencing. Further qRT-PCR assays confirmed 3 down-regulated miRNAs (miR-34c-5p, miR-375 and miR-449c-5p), 4 up-regulated miRNAs (miR-205-5p, miR-92a-3p, miR-193b-3p and miR-27a-5p). Additionally, the low level of miR-34c-5p (miR-34c) was significantly correlated with advanced TNM stage. GO and KEGG enrichment analyses showed that 914 target genes were involved in cell cycle, cytokine secretion and tumor immunology, and so on. IPA revealed that cancer was the top disease associated with those dysregulated miRNAs, and the genes regulated by miR-34c were in the center of miRNA-mRNA regulatory network, including TP53, CCND1, CDK6, MET and BCL2, and the PI3K/AKT/ mTOR signaling was regarded as a significant function pathway in this network.
  
  
  CONCLUSIONS
  Our study presents the current knowledge of miRNA regulatory network in NPC with combination of bioinformatics analysis and literature research. The hypothesis of miR-34c regulatory pathway may be beneficial in guiding further studies on the molecular mechanism of NPC tumorigenesis.
authors.affiliation: Department of Otolaryngology, Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. wf493649053@qq.com.
authors.forename: Fan
authors.initials: F
authors.lastname: Wang
authors.affiliation: Department of Otolaryngology, Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. lujuanqz@163.com.
authors.forename: Juan
authors.initials: J
authors.lastname: Lu
authors.affiliation: Department of Otolaryngology, Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. 418897077@qq.com.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Peng
authors.affiliation: Department of Otolaryngology, Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. 420242012@qq.com.
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Otolaryngology, Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. liux1218@126.com.
authors.forename: Xiong
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Otolaryngology, Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. 1028192485@qq.com.
authors.forename: Xiaomei
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Guangdong No.2 District, BGI Genomics Co., Ltd, Shenzhen, 518083, China. jiangyiqi@genomics.cn.
authors.forename: Yiqi
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Department of Otolaryngology, Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. li321162@qq.com.
authors.forename: Xiangping
authors.initials: X
authors.lastname: Li
authors.affiliation: School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515, China. zhang20051005@126.com.
authors.forename: Bao
authors.initials: B
authors.lastname: Zhang
mesh_terms: D002277:Carcinoma; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D008875:Middle Aged; D000077274:Nasopharyngeal Carcinoma; D009303:Nasopharyngeal Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D009304:Nasopharyngitis / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs