Research Papers:

Genomic characterization of human papillomavirus-positive and -negative human squamous cell cancer cell lines

Nene N. Kalu, Tuhina Mazumdar, Shaohua Peng, Li Shen, Vaishnavi Sambandam, Xiayu Rao, Yuanxin Xi, Lerong Li, Yuan Qi, Frederico O. Gleber-Netto, Ameeta Patel, Jing Wang, Mitchell J. Frederick, Jeffrey N. Myers, Curtis R. Pickering and Faye M. Johnson _

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Oncotarget. 2017; 8:86369-86383. https://doi.org/10.18632/oncotarget.21174

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Nene N. Kalu1,6, Tuhina Mazumdar1, Shaohua Peng1, Li Shen2, Vaishnavi Sambandam1, Xiayu Rao2, Yuanxin Xi2, Lerong Li2, Yuan Qi2, Frederico O. Gleber-Netto3, Ameeta Patel3, Jing Wang2,4, Mitchell J. Frederick5, Jeffrey N. Myers3,4, Curtis R. Pickering3,4 and Faye M. Johnson1,4

1Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA

2Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA

3Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA

4The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA

5Department of Otolaryngology, Baylor College of Medicine, Houston, Texas, USA

6Current/Present address: Lonza Viral Therapy, Houston, Texas, USA

Correspondence to:

Faye M. Johnson, email: [email protected]

Keywords: human papillomavirus, cervical cancer, head and neck squamous cell carcinoma, cell lines, mutation

Received: June 22, 2017    Accepted: August 21, 2017    Published: September 21, 2017


Human cancer cell lines are the most frequently used preclinical models in the study of cancer biology and the development of therapeutics. Although anatomically diverse, human papillomavirus (HPV)-driven cancers have a common etiology and similar mutations that overlap with but are distinct from those found in HPV-negative cancers. Building on prior studies that have characterized subsets of head and neck squamous cell carcinoma (HNSCC) and cervical squamous cell carcinoma (CESC) cell lines separately, we performed genomic, viral gene expression, and viral integration analyses on 74 cell lines that include all readily-available HPV-positive (9 HNSCC, 8 CESC) and CESC (8 HPV-positive, 2 HPV-negative) cell lines and 55 HPV-negative HNSCC cell lines. We used over 700 human tumors for comparison. Mutation patterns in the cell lines were similar to those of human tumors. We confirmed HPV viral protein and mRNA expression in the HPV-positive cell lines. We found HPV types in three CESC cell lines that are distinct from those previously reported. We found that cell lines and tumors had similar patterns of viral gene expression; there were few sites of recurrent HPV integration. As seen in tumors, HPV integration did appear to alter host gene expression in cell lines. The HPV-positive cell lines had higher levels of p16 and lower levels of Rb protein expression than did the HPV-negative lines. Although the number of HPV-positive cell lines is limited, our results suggest that these cell lines represent suitable models for studying HNSCC and CESC, both of which are common and lethal.

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