Integration of human papillomavirus (HPV) genomes into cellular chromatin is common in HPV-associated cancers. Integration is random, and each site is unique depending on how and where the virus integrates. We recently showed that tandemly integrated HPV16 could result in the formation of a super-enhancer-like element that drives transcription of the viral oncogenes. Here, we characterize the chromatin landscape and genomic architecture of this integration locus to elucidate the mechanisms that promoted de novo super-enhancer formation. Using next-generation sequencing and molecular combing/fiber-FISH, we show that ~26 copies of HPV16 are integrated into an intergenic region of chromosome 2p23.2, interspersed with 25 kb of amplified, flanking cellular DNA. This interspersed, co-amplified viral-host pattern is frequent in HPV-associated cancers and here we designate it as Type III integration. An abundant viral-cellular fusion transcript encoding the viral E6/E7 oncogenes is expressed from the integration locus and the chromatin encompassing both the viral enhancer and a region in the adjacent amplified cellular sequences is strongly enriched in the super-enhancer markers H3K27ac and Brd4. Notably, the peak in the amplified cellular sequence corresponds to an epithelial-cell-type specific enhancer. Thus, HPV16 integration generated a super-enhancer-like element composed of tandem interspersed copies of the viral upstream regulatory region and a cellular enhancer, to drive high levels of oncogene expression. Author summary Oncogenic human papillomavirus (HPV) infection is responsible for ~5% human cancers. A key event in the development of many of these cancers is integration of the viral genome into host chromatin. Integration results in dysregulated expression of the viral oncogenes, which promotes unregulated cellular division and the accumulation of cellular mutations, ultimately leading to cancer. Genetic rearrangement and/or amplification of cellular sequences flanking sites of integration are frequent in HPV positive tumors, and this can influence transcription of the viral oncogenes from integrated loci. We show an example where the HPV16 genome integrated adjacent to a cellular, tissue-specific enhancer and subsequently the viral DNA and flanking cellular sequences were co-amplified into a tandemly interspersed viral-cellular sequence array. The genetic and epigenetic signature of this site promoted the formation of a de novo super-enhancer-like element to drive high viral oncogene expression. This provides insight into the genesis of super-enhancer-like elements and is a novel mechanism by which HPV integration can promote oncogenesis.
【초록키워드】 Cancer, Genome, Genetic, Transcription, mutations, Infection, virus, amplification, Viral, cancers, Next-generation sequencing, molecular, genomic, expression, Epigenetic, mechanism, marker, cellular, BRD4, integration, viral genome, HPV, tumors, human papillomavirus, locus, chromosome, accumulation, sequence, loci, random, positive, chromatin, element, de novo, cellular DNA, genesis, H3K27ac, intergenic region, oncogene, oncogenesis, papillomavirus, super-enhancer, viral DNA, enhancer, upstream, regulatory region, transcript, Host, human cancers, responsible, amplified, example, composed, provide, unique, expressed, promote, dysregulated, Type, promoted, 【제목키워드】 Viral, expression, cellular, HPV, enhancer, generate,