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Transcriptome profiling of the cancer and adjacent nontumor tissues from cervical squamous cell carcinoma patients by RNA sequencing

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Tumor Biology

Abstract

Cervical cancer is the third most common cancer and the fourth leading cause of cancer deaths among women in the world. The discovery of vital diagnostic and therapeutic markers against cervical squamous cell carcinoma (CSCC) would broaden our understanding on the molecular basis of CSCC. In this study, we thoroughly analyzed the transcriptome of CSCC and matched adjacent nontumor (ATN) tissue. RNA sequencing was performed to screen the differentially expressed genes (DEGs) of three pairs of CSCC and ATN tissues. Functional enrichment analysis was used to uncover the biological functions of DEGs. Protein interaction network was carried out to reveal interaction of DEGs. Quantitative real-time PCR was conducted to validate the expression of DEGs. Immunohistochemistry was used to detect the relationship between clinicopathological parameters of CSCC and DEGs. There were a total of 347 significantly common DEGs in the three paired examples, including 104 consistent upregulated and 148 consistent downregulated DEGs. The 347 DEGs were categorized into 73 functional categories by Gene Ontology (GO) analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis suggested six significantly signal pathways. The protein interaction network uncovered three important DEGs, including retinol dehydrogenase 12 (RDH12), ubiquitin D (UBD), and serum amyloid A1 (SAA1). We found that RDH12 expression was decreased in 74.5 % of CSCC tissues. RDH12 expression was negatively associated with tumor size and depth of cervical invasion. The UBD was overexpressed in 61.7 % of CSCC tissues and was positively related with tumor size and lymphatic metastasis. The SAA1 protein was overexpressed in 57.4 % of CSCC tissues and was positively related with clinicopathological parameters of tumor size, lymphatic metastasis, and depth of cervical invasion. The RDH12, UBD, and SAA1 genes might participate in the progression of CSCC.

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Acknowledgments

This research is supported by the National Natural Science Foundation of China (81472446).

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Authors and Affiliations

  1. Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, No. 1 Shuai Fu Yuan, Wang Fu Jing Street, Beijing, 100730, People’s Republic of China

    Guo Peng, Wang Dan, Yang Junjun, Ren Tong & Xiang Yang

  2. CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People’s Republic of China

    Wu Jun & Zhu Baoli

Authors
  1. Guo Peng
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  2. Wang Dan
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  3. Wu Jun
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  4. Yang Junjun
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  7. Xiang Yang
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Corresponding authors

Correspondence to Zhu Baoli or Xiang Yang.

Electronic supplementary material

Below is the link to the electronic supplementary material.

S1

The list of differentially expressed genes. (XLS 227 kb)

S2

The list of functional categories of differentially expressed genes. (XLS 83 kb)

S3

Protein-protein interaction network construction of CSCC. The 13 cervical cancer related genes from NCI are filled with blue. Three novel cervical cancer related genes identified in our study are filled with red. The other detected DEGs in the PPI network are filled with green. Each link between two nodes corresponds to a direct interaction between the two genes according to HPRD database (GIF 2948 kb)

High resolution image (TIFF 3982 kb)

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Peng, G., Dan, W., Jun, W. et al. Transcriptome profiling of the cancer and adjacent nontumor tissues from cervical squamous cell carcinoma patients by RNA sequencing. Tumor Biol. 36, 3309–3317 (2015). https://doi.org/10.1007/s13277-014-2963-0

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  • DOI: https://doi.org/10.1007/s13277-014-2963-0

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