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Genome-wide gene expression profiling of tongue squamous cell carcinoma by RNA-seq

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Abstract

Objective

Tongue squamous cell carcinoma (TSCC) is significantly more malignant than other type of oral squamous cell carcinoma (OSCC). In this study, we aimed to identify specific global gene expression signatures of TSCC to investigate the more invasive behavior of the deeply infiltrating cancer.

Methods

Using RNA-seq technology, we detected gene expression of 20 TSCCs, 20 matched paratumor tissues, and 10 healthy normal mucosa tissues. Enrichment analysis of gene ontology (GO) and pathway was conducted using online tools DAVID for the dysregulated genes. Additionally, we performed the quantitative real-time RT-PCR (qRT-PCR) to validate the findings of RNA-Seq in 10 samples of TSCC, matched paratumor, and normal mucosa, respectively.

Results

We detected 252 differentially expressed genes (DEGs) between TSCC and matched paratumor tissue, including 117 up-regulated and 135 down-regulated genes. For comparison between TSCC and normal mucosa, 234 DEGS were identified, consisting of 67 up-regulated and 167 down-regulated genes. For both two comparisons, GO categories of muscle contraction (GO: 0006936), epidermis development (GO: 0008544), epithelial cell differentiation (GO: 0030855), and keratinization (GO: 0031424) were commonly enriched. Altered gene expression affected some cancer-related pathways, such as tight junction. The qRT-PCR validation showed that gene expression patterns of FOLR1, NKX3-1, TFF3, PIGR, NEFL, MMP13, and HMGA2 were fully in concordance with RNA-Seq results.

Conclusion

Findings in this study demonstrated the genetic and molecular alterations associated with TSCC, providing new clues for understanding the molecular mechanisms of TSCC pathogenesis.

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Authors and Affiliations

  1. Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, 410011, China

    Hai Xia Zhang, Chao Deng, Yan He, Ye Qian Feng, Jin An Ma & Chun Hong Hu

  2. Department of Orthodontics, Xiangya Stomatological Hospital & School of Stomatology, Central South University, Changsha, Hunan Province, 410078, China

    Ou Sheng Liu

  3. Department of Oral and Maxillofacial Surgery, Xiangya Stomatological Hospital & School of Stomatology, Central South University, Changsha, Hunan Province, 410078, China

    Zhan Gui Tang

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  1. Hai Xia Zhang
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  4. Yan He
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Correspondence to Chun Hong Hu or Zhan Gui Tang.

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

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Informed consent was obtained from all individual participants included in the study.

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Zhang, H.X., Liu, O.S., Deng, C. et al. Genome-wide gene expression profiling of tongue squamous cell carcinoma by RNA-seq. Clin Oral Invest 22, 209–216 (2018). https://doi.org/10.1007/s00784-017-2101-7

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  • DOI: https://doi.org/10.1007/s00784-017-2101-7

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