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APOBEC Mutagenesis is Concordant Between Tumor and Viral Genomes in HPV Positive Head and Neck Squamous Cell Carcinoma

By Daniel L Faden, Krystle A. Lang Kuhs, Maoxuan Lin, Adam Langenbucher, Maisa Pinheiro, Meredith Yeager, Michael Cullen, Joseph F Boland, Mia Steinberg, Sara Bass, James S. Lewis, Michael S Lawrence, Robert L. Ferris, Lisa Mirabello

Posted 27 Feb 2021
bioRxiv DOI: 10.1101/2021.02.27.433168

APOBEC (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like) is a major mutagenic source in human papillomavirus positive oropharyngeal squamous cell carcinoma (HPV+ OPSCC). Why APOBEC mutations predominate in HPV+OPSCC remains an area of active investigation. Prevailing theories focus on APOBECs role as a viral restriction agent. APOBEC-induced mutations have been identified in both human cancers and HPV genomes, but whether they are directly linked in HPV+OPSCCs remains unknown. We performed sequencing of host somatic exomes, transcriptomes and HPV16 genomes from 79 HPV+ OPSCC samples, quantifying APOBEC mutational burden and activity in both the host and virus. APOBEC was the dominant mutational signature in somatic exomes. APOBEC vulnerable PIK3CA hotspot mutations were exclusively present in APOBEC enriched samples. In viral genomes, there was a mean (range) of 5 (0-29) mutations per genome. Mean (range) of APOBEC mutations in the viral genomes was 1 (0-5). Viral APOBEC mutations, compared to non-APOBEC mutations, were more likely to be low-variant allele frequency mutations, suggesting that APOBEC mutagenesis is actively occurring in viral genomes during infection. Paired host and viral analyses revealed that APOBEC-enriched tumor samples had higher viral APOBEC mutation rates (p=0.028), and APOBEC-associated RNA editing (p=0.008) suggesting that APOBEC mutagenesis in host and viral genomes are directly linked. Using paired sequencing of host somatic exomes, transcriptomes, and viral genomes from HPV+OPSCC samples, here, we show concordance between tumor and viral APOBEC mutagenesis, suggesting that APOBEC-mediated viral restriction results in off-target host-genome mutations. These data provide a missing link connecting APOBEC mutagenesis in host and virus and support a common mechanism driving APOBEC dysregulation.

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