Abstract 4147: Mate pair sequencing reveals that human papillomavirus integration into the human genome in oropharyngeal squamous cell carcinoma is rare and different from cervical cancer

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA In spite of decreases in the incidence of smoking in the United States over the past several decades, the incidence of oropharyngeal squamous cell carcinoma (OPSCC) has been increasing. This is presumably due to an increase in the incidence of human papillomavirus (HPV)-positive OPSCC. The model for how HPV contributes to cancer development is based upon studies characterizing cervical cancer. In cervical cancer almost all invasive cancers have HPV integrated into the human genome with loss of episomal copies of HPV. The site of integration is usually within the HPV E2 gene which functions as a repressor of the two key HPV oncoproteins, E6 and E7. The resulting over-production of E6 and E7 inactivates two key pathways which results in genomic instability and additional down-stream alterations that eventually leads to invasive cervical cancer. In order to definitively test whether this model is indeed true for OPSCC we performed mate-pair next generation sequencing on both tumor and adjacent normal tissues from 20 OPSCC patients: 7 were HPV16-positive and had high expression of the E6 and E7 transcripts; 6 were HPV-positive but with low E6 and E7 transcription; and as a control we also analyzed 7 HPV16-negative tumors. This high throughput technology was able to successfully detect all HPV integration events into the human genome as well as HPV bridged coverage from these samples with high specificity. Just a single HPV-positive tumor with high oncogene expression had HPV integration events (two), but this patient also had a very high copy number of episomal HPV sequences. A single HPV-positive tumor with low oncogene expression had one HPV integration event, but no episomal HPV sequences present. One of the HPV16-negative tumors had a single HPV26 integration with no episomal HPV sequences. None of the matched normal samples had either HPV integrations or an appreciable amount of episomal HPV sequences present. Thus, only 21.4% of HPV-positive OPSCCs had integrations event. All four integrations were validated by PCR and Sanger sequencing which revealed that none of them interrupted the HPV E2 gene. All four of the integrations occurred next to human genes that have been found to be altered in different cancers. Our results suggest that the role that HPV plays in OPSCC may be quite distinct from what is observed in cervical cancer. The results also demonstrate that not all HPV-positive OPSCCs have HPV in the same physical state. It will thus be interesting to compare the distinct groups of HPV-positive OPSCCs with respect to overall clinical prognosis. Citation Format: Ge Gao. Mate pair sequencing reveals that human papillomavirus integration into the human genome in oropharyngeal squamous cell carcinoma is rare and different from cervical cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4147. doi:10.1158/1538-7445.AM2014-4147