Abstract 1515: Identification and characterization of HPV-host fusion transcripts in HNSCCs
Authors: Koneva Lada A. , Zhang Yanxiao , Hall Pelle , Virani Shama , Virani Alisha , Carey Thomas E. , Rozek Laura S. , Sartor Maureen A. 
Published: July 2016

Introduction

Head and neck squamous cell carcinoma (HNSCC) is the sixth most incident cancer worldwide. Human papillomavirus (HPV) is implicated in at least 70% of oropharyngeal squamous cell carcinomas in the US. HPV genomic integration events are a likely critical step in progression to cancer and occur as a consequence of HPV oncogene-induced chromosomal instability. The majority of viral integration events in the human genome appear to occur within or near genic regions. Identified HPV integration events in HNSCC were associated with alterations in DNA copy number, mRNA transcript abundance and splicing, and inter-/intrachromosomal rearrangements.

Materials and methods

We analyzed 84 HPV-positive HNSCC samples collected at the University of Michigan (18 tumors) and from The Cancer Genome Atlas (66 tumors). We used VirusSeq software for detection of integration events. Integrations were evidenced by host-virus fusion transcripts in RNA-seq, considering only breakpoints supported by at least four discordant read pairs and at least one junction spanning read.

Results

We identified 50 integration-positive tumors, which consisted of 41 with HPV16, one tumor with HPV18, 5 tumors with HPV33 and 3 with HPV35. We found an overall 271 breakpoints of integration within or near 83 human genes. Fusion virus-host transcripts with breakpoints within E6 and E7 HPV oncogenes were more common (59.3%) compared with breakpoints into other viral genes: E1 and E2 (19%), E4 and E5 (16.8%), L1 and L2 (4.7%).

The detected viral integration events were widespread across the human genome with a few hotspots of recurrent integrations in genic regions at 1p36, 9p24, and 13p22. After accounting for regions covered by the data, we did not find an association of integration sites with aphidicolin-induced common fragile sites (CFSs), as observed for HPV integration sites in cervical cancer.

Analysis of the protein interaction network constructed from the 83 host genes harboring viral integrants showed that 56 of them were linked into a highly connected sub-network with direct interactions. ETS2, TP63, FOXA1, CTGF and KLF5 were hubs in this network. The genes were statistically enriched for cancer genes known as important in “Head and Neck Neoplasms”(p = 1.74E-11).

Conclusion

HPV integration events in HNSCC are largely different from those common to cervical cancers. While TP63 appears to be a recurrent target in both cervical cancer and HNSCC, HNSCCs have a surprisingly high percent of integration events in known HNSCC-related genes. Overall, our results suggest that there is strong selective pressure for integration events that occur in HNSCC relevant genes.

Citation Format: Lada A. Koneva, Yanxiao Zhang, Pelle Hall, Shama Virani, Alisha Virani, Thomas E. Carey, Laura S. Rozek, Maureen A. Sartor. Identification and characterization of HPV-host fusion transcripts in HNSCCs. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1515.