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Am J Otolaryngol. 2019 Jul - Aug;40(4):547-554. doi: 10.1016/j.amjoto.2019.04.015. Epub 2019 Apr 23.

The molecular differences between human papillomavirus-positive and -negative oropharyngeal squamous cell carcinoma: A bioinformatics study.

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The 16th Ward, Department of Ear, Nose and Throat (ENT), Daqing Oilfield General Hospital, Zhongkang Street No. 9, Saertu District, 163000, Daqing City, Heilongjiang Province, China.
Department of Stomatology, Northeast Petroleum University Affiliated Hospital, Fazhan Road, High Tech District, 163000 Daqing City, Heilongjiang Province, China.
Department of Stomatology, The Heping Affiliated Hospital of Changzhi Medical College, Changzhi City, Shanxi Province, China.
Faculty of Dentistry, University of Hong Kong, Hong Kong, China; Dr D Y Patil Dental College and Hospital, Dr D Y Patil Vidyapeeth, Pimpri, Pune, India.
Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany.
Saxon Incubator for Clinical Translation/Translational Centre for Regenerative Medicine, Leipzig University, Phillip-Rosenthal-Str. 55, Leipzig 04103, Germany.
Genomap Technologies, Kongjiang Road 1500, Yangpu District, Shanghai, China.
School of Dentistry, University of Michigan, USA.
Heart Center Leipzig, University of Leipzig, Strümpellstr. 39, 04289 Leipzig, Germany.
Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany. Electronic address:
Laboratory of Molecular Cell Biology, Beijing Tibetan Hospital, China Tibetology Research Center, 218 Anwaixiaoguanbeili Street, Chaoyang, Beijing 100029, China. Electronic address:



To investigate the genetic and epigenetic differences between human papillomavirus (HPV)-positive oropharyngeal squamous cell carcinoma (OPSCC) and HPV-negative OPSCC.


Microarray data of HPV-positive and -negative OPSCC were retrieved from NCBI GEO datasets. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DE-miRNAs) were identified by performing differential expression analysis. A functional enrichment analysis was performed to explore the biological processes and signaling pathways that DEGs and DE-miRNAs were involved in, respectively. A protein-protein interaction (PPI) network of DEGs was constructed to identify hub genes. miRNA-target network and miRNA-miRNA functional synergistic network were each constructed in order to identify risk-marker miRNAs. An miRNA-target-pathway network was constructed in order to explore the function of identified risk-marker miRNAs.


Microarray data from 3 datasets (GSE39366, GSE40774, and GSE55550) was included and analyzed. The PPI network identified 3 hub genes (VCAM1, UBD, and RPA2). MiR-107 and miR-142-3p were found to play the most significant role in both the DE-miRNA-target network as well as in the miRNA-miRNA functional synergistic network. MiR-107 was involved in HPV-induced tumorigenesis by targeting many genes (CAV1, CDK6, MYB, and SERPINB5) and regulating the p53 signaling pathway, the PI3K-Akt signaling pathway, and the autophagy pathway. In addition, miR-142-3p was implicated in HPV-induced tumorigenesis by targeting the PPFIA1 gene and regulating transcriptional dysregulation and other cancerous pathways.


Three genes (VCAM1, UBD, and RPA2), two miRNAs (miR-107 and miR-142-3p), and four pathways (p53, PI3K-Akt, autophagy, and transcription dysregulation in cancer) were identified to play critical roles in distinguishing HPV-positive OPSCC from HPV-negative OPSCC.


Genes; Human papillomavirus; Oropharyngeal squamous cell carcinoma; Pathways; miRNAs

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