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Comprehensive analysis of gene expression and DNA methylation for human nasopharyngeal carcinoma

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European Archives of Oto-Rhino-Laryngology Aims and scope Submit manuscript

Abstract

Purpose

Nasopharyngeal carcinoma (NPC) is one of the most malignant head and neck carcinomas with unique epidemiological features. In this study, we aimed to identify the novel NPC-related genes and biological pathways, shedding light on the potential molecular mechanisms of NPC.

Methods

Based on Gene Expression Omnibus (GEO) database, an integrated analysis of microarrays studies was performed to identify differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in NPC compared to normal control. The genes which were both differentially expressed and differentially methylated were identified. Functional annotation and protein–protein interaction (PPI) network construction were used to uncover biological functions of DEGs.

Results

Two DNA methylation and five gene expression datasets were incorporated. A total of 1074 genes were up-regulated and 939 genes were down-regulated in NPC were identified. A total of 719 differential methylation CpG sites (DMCs) including 1 hypermethylated sites and 718 hypomethylated sites were identified. Among which, 11 genes were both DEGs and DMGs in NPC. Pathways in cancer, p53 signaling pathway and Epstein–Barr virus infection were three pathways significantly enriched pathways in DEmRNAs of NPC. The PPI network of top 50 DEGs were consisted of 191 nodes and 191 edges.

Conclusions

Our study was helpful to elucidate the underlying mechanism of NPC and provide clues for therapeutic methods.

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Authors and Affiliations

  1. Department of Otolaryngology, The First People’s Hospital of Jining, No. 6 Jiankang Road, Jining, 272011, Shandong, China

    Hu Li, Jun An, Ming-lei Liu, Wei Li, Jing-E. Zhang & Ping-ping Wu

  2. Department of Gynecology, Maternal and Child Health Hospital of RenCheng District, Jining, Jining, Shandong, China

    Fu-Ling Wang

  3. Department of Laboratory, The First People’s Hospital of Jining, Jining, Shandong, China

    Liang-peng Shan

Authors
  1. Hu Li
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  2. Fu-Ling Wang
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  3. Liang-peng Shan
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  4. Jun An
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  5. Ming-lei Liu
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  6. Wei Li
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  7. Jing-E. Zhang
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  8. Ping-ping Wu
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Corresponding authors

Correspondence to Jing-E. Zhang or Ping-ping Wu.

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Li, H., Wang, FL., Shan, Lp. et al. Comprehensive analysis of gene expression and DNA methylation for human nasopharyngeal carcinoma. Eur Arch Otorhinolaryngol 276, 2565–2576 (2019). https://doi.org/10.1007/s00405-019-05525-2

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  • DOI: https://doi.org/10.1007/s00405-019-05525-2

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