A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing

Abstract

Background. Next-generation sequencing of cancers has identified important therapeutic targets and biomarkers. The goal of this pilot study was to compare the genetic changes in a human papillomavirus- (HPV-)positive and an HPV-negative head and neck tumor. Methods. DNA was extracted from the blood and primary tumor of a patient with an HPV-positive tonsillar cancer and those of a patient with an HPV-negative oral tongue tumor. Exome enrichment was performed using the Agilent SureSelect All Exon Kit, followed by sequencing on the ABI SOLiD platform. Results. Exome sequencing revealed slightly more mutations in the HPV-negative tumor (73) in contrast to the HPV-positive tumor (58). Multiple mutations were noted in zinc finger genes (ZNF3, 10, 229, 470, 543, 616, 664, 638, 716, and 799) and mucin genes (MUC4, 6, 12, and 16). Mutations were noted in MUC12 in both tumors. Conclusions. HPV-positive HNSCC is distinct from HPV-negative disease in terms of evidence of viral infection, p16 status, and frequency of mutations. Next-generation sequencing has the potential to identify novel therapeutic targets and biomarkers in HNSCC.

Figure 1

Tumors from two patients were sectioned. Slices were stained with ((a) and (b)) H&E, ((c) and (d)) p16, or ((e) and (f)) HPV in situ hybridization. Panels represent magnified images of the complete section (inset).

Figure 2

PCR confirmation of the presence of HPV type 16 DNA in patient 1 and the absence of HPV type 16 sequences in patient 2.

Figure 3

Detection of HPV 16 sequences with the exome captures of the four patient samples. Short read sequences generated from the exome sequencing data denoted by the small bars were found exclusively in the DNA from the HPV-positive tumor but not in the matched blood from the same patient or the HPV-negative patient's tumor or blood with the exception of the nonspecific poly-A signal.