HPV-associated head and neck cancer: molecular and nano-scale markers for prognosis and therapeutic stratification

Abstract

Over the last 10 years, it has become clear that patients with head and neck cancer can be stratified into two distinct subgroups on the basis of the etiology of their disease. Patients with human papillomavirus-related cancers have significantly better survival rates and may necessitate different therapeutic approaches than those with tobacco and/or alcohol related cancers. This review discusses the various biomarkers currently in use for identification of patients with HPV-positive cancers with a focus on the advantages and limitations of molecular and nano-scale markers.

Keywords: biomarkers; head and neck cancer; human papillomavirus; in situ hybridization; next generation sequencing.

Figure 1.

A type specific viral genome is digested with chosen restriction enzymes and resulting oligonucleotide fragments are radioactively labeled. Simultaneously, tumor DNA is also subjected to restriction digestion. Tumor DNA fragments are separated by agarose electrophoresis and transferred to a nitrocellulose membrane. Radioactively labeled probes are allowed to hybridize with cellular DNA, washed, and detected via overnight exposure of film to the membrane. Bands of HPV DNA present within the original tumor DNA can be detected due to hybridization with labeled probes.

Figure 2.

Tumor blocks are unmasked and allowed to hybridize with HPV type specific probes prior to fixation and detection via either fluorescent or bright field microscopy. HPV DNA sequences within the nucleus of cells can be identified.

Figure 3.

(A) Polymerase chain reaction (PCR) or reverse transcriptase PCR utilize either tumor DNA or cDNA that is reverse transcribed from tumor RNA. Oligonucleotide probes specific for a region of DNA are then used to amplify a given sequence region. The use of a labeled probe (star) allows for real-time detection of amplification products (B).

Figure 4.

Next generation sequencing utilizes high-throughput methods to simultaneously determine the oligonucleotide sequence of hundreds or thousands of DNA fragments generated following restriction digestion of tumor DNA or reverse transcription of tumor RNA. Newer methods are also able to sequence RNA directly. Each commercial platform utilizes a different specific technology (black box) to determine the nucleotide sequence.