Robust HPV-16 Detection Workflow for Formalin-Fixed Cancer Tissue and Its Application for Oral Squamous Cell...

Area of Science:

• Oncology
• Virology
• Molecular Biology

Background:

• Virus-related cancers, including those caused by human papillomavirus (HPV), pose a significant global health burden.
• Persistent HPV infection can lead to oncogenic transformation and malignancy.
• Accurate detection of HPV in cancer specimens is crucial for understanding disease mechanisms.

Purpose of the Study:

• To develop a robust method for detecting human papillomavirus type 16 (HPV-16) in formalin-fixed cancer specimens.
• To investigate the frequency and integration patterns of HPV-16 in oral squamous cell carcinoma (OSCC).

Main Methods:

• A multiplex polymerase chain reaction (PCR) assay covering the entire HPV-16 genome was developed.
• A DNA quality check step was incorporated to prevent false negatives.
• The protocol was validated on oropharyngeal cancer tissues and subsequently applied to a cohort of OSCC samples.

Main Results:

• The multiplex PCR detected HPV-16 in a subset of OSCC cases, with variable positivity confirmed by droplet digital PCR.
• Analysis revealed the integration of a deleted HPV-16 genome into the TMEM94 gene on chromosome 17 in an OSCC case.
• This represents the first documented evidence of HPV-16 genome integration within OSCC cells, including its complete viral sequence.

Conclusions:

• The developed HPV-16 detection protocol is applicable to various cancer tissues.
• This method can aid in analyzing the association between HPV-16 infection and different cancer types.
• The findings highlight a novel mechanism of HPV-16 integration in OSCC.