Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers

Abstract

Human papillomavirus (HPV) causes 5% of all cancers and frequently integrates into host chromosomes, but the impacts of integration in tumorigenesis remain unclear. Analysis of 105 HPV-positive oropharyngeal cancers by whole genome sequencing detects viral integration in 77%, revealing five statistically significant integration hotspots near genes that regulate epithelial stem cell maintenance (i.e. SOX2, TP63, FGFR, MYC) and immune evasion (i.e. CD274). Somatic hyperamplification is enriched 16-fold near HPV integrants, and the extent of focal host genomic instability increases with local density of HPV integrants. Genes expressed at extreme outlier levels are increased 86-fold within +/- 150 kb of integrants. Across 95% of tumors with integration, host gene transcription is disrupted via intragenic integrants, chimeric transcription, outlier expression, gene breaking and/or de novo expression of noncoding or imprinted genes. We conclude that HPV integration contributes substantively to cancer development by causing extensive disruption of host genome structure and gene expression.

Intratumoral heterogeneity and clonal evolution induced by HPV integration

“…Our analysis of 105 HPV-positive oropharyngeal cancers by WGS identified HPV-host insertional breakpoints that directly flank, bridge, or map within host genomic regions enriched with SVs and CNVs (5). To resolve genomic rearrangements at sites of HPV integration, we selected five HPV-positive primary oropharyngeal cancers and four HPV-positive human cell lines, 93-VU-147T (hereafter VU147) (12), HeLa (13), GUMC-395 (14), and HTEC (15), for WGS using Illumina paired-end sequencing and LR-seq using the PacBio and ONT platforms.…”

“…Such ecDNA presence has been linked with poorer survival (36). By contrast, reported associations between HPV integration and survival in oropharyngeal cancer are inconsistent (5,37,38).…”

“…The viral genome is maintained early in infection as an ~8-kilobase-pair (kb) extrachromosomal circular DNA (ecDNA) episome. In a majority of subsequent cancers, the viral genome has integrated into the host genome (2)(3)(4)(5). HPV integration promotes tumorigenesis by increasing expression and stability of transcripts encoding the E6 and E7 oncoproteins (6), which target tumor suppressors p53 and pRb for degradation, respectively (7,8).…”

“…HPV integration promotes tumorigenesis by increasing expression and stability of transcripts encoding the E6 and E7 oncoproteins (6), which target tumor suppressors p53 and pRb for degradation, respectively (7,8). Recent whole genome sequencing (WGS) analyses of cervical and oropharyngeal cancers revealed that HPV integrants are enriched in genomic regions with structural variants (SVs) and copy number variants (CNVs) (2,4,5,9). Diverse genetic consequences of HPV integration have been identified, including dysregulated host gene expression near integrants (2)(3)(4)(5).…”

“…Recent whole genome sequencing (WGS) analyses of cervical and oropharyngeal cancers revealed that HPV integrants are enriched in genomic regions with structural variants (SVs) and copy number variants (CNVs) (2,4,5,9). Diverse genetic consequences of HPV integration have been identified, including dysregulated host gene expression near integrants (2)(3)(4)(5).…”