Gao, Ge

Abstract 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

Abstract Human papillomavirus (HPV) appears to be responsible for dramatic increases in the incidence of oropharyngeal squamous cell carcinoma (OPSCC) in the United States in the last two decades, in spite of decreases in the incidence of smoking. It is generally assumed that the role of HPV in the development of OPSCC is identical to the one that it plays in cervical cancer where HPV infection followed by integration into the host genome and the subsequent increased expression of the E6 and E7 oncoproteins leads to increased genomic instability. The common fragile sites (CFSs) are highly unstable chromosomal regions that will be particularly sensitive to increased genomic instability and they are also hot-spots for viral integrations in cervical cancer. The CFS regions span many megabases and many of them also span extremely large genes, a number of which have been demonstrated to function as important tumor suppressors. We therefore examined the expression of very large genes in OPSCC. An analysis of RNAseq data generated on 11 OPSCCs and matched normal oropharyngeal tissue from the same patients revealed that some of the tumors had greatly decreased expression for many of the largest genes. The two genes with the greatest decreases in expression in the tumors as compared to matched normal were the known tumor suppressor PARK2 and the putative tumor suppressor DLG2, but three other large CFS genes: CTNNA3, LRP1B and DMD, and one large gene not yet precisely localized within a CFS region: PDE4D, also had much more decreased expression than any of the other large genes. Real-time RT-PCR was used to measure the expression of these six genes in a much larger number of OPSCC tumor-normal pairs. The expression of these six genes was concordant in most OPSCCs. An individual tumor generally had either decreased expression of these six genes, no changes in the expression of these genes or increased expression of all six genes. When the tumors were grouped with respect to which ones were HPV-positive or HPV-negative we observed that 40% of the HPV-positive OPSCCs had greatly decreased expression (more than 100-fold) for all six genes. Half of the HPV-negative tumors had decreased expression of these six genes, but the amount of decreased expression was much more modest (4-16 fold). Most exciting, however was that 7 of the 12 HPV-positive tumors, and three of the four of the HPV-negative patients that had decreased expression of these genes were from patients who had tumor recurrence. In contrast only one of 18 patients whose tumors did not have decreased expression of the large genes had tumor recurrence. The loss of expression of multiple large genes, many of which are derived from CFS regions, could thus be a powerful predictor for which patients will have tumor recurrence. These results also suggest a linkage between HPV-induced chromosomal instability and dramatic decreases in the expression of multiple CFS genes in some OPSCCs. Citation Format: David I. Smith, Ge Gao, Nicole Tombers, Jan Kasperbauer, Vivian Wang. Human papillomavirus and the inactivation of expression of multiple large common fragile site genes in oropharyngeal squamous cell carcinoma. [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 582. doi:10.1158/1538-7445.AM2014-582