Human papillomavirus (HPV) integration is a critical step in cervical cancer development, while the oncogenic mechanism in genome-wide transcriptional level is still poorly understood. In this study, we employed integrative analysis on multi-omics data of cervical cancer cell lines. Through HPV integration detection, super enhancer (SE) identification, SE-associated gene expression and extrachromosomal DNA (ecDNA) investigation, we aimed to explore the genome-wide transcriptional influence of HPV integration. We identified 5 high-ranking cellular super enhancers generated by HPV integration (the HPV breakpoint induced cellular super enhancers, BP-cSE), leading to intra-chromosomal and inter-chromosomal regulations of chromosomal genes. The pathway analysis showed the dysregulated chromosomal genes were correlated to cervical cancer associated pathways. Importantly, we demonstrated that BP-cSE existed in the HPV-host ecDNA, explaining above transcription alterations. Our results suggest that HPV integration generates cellular super enhancers and functions as ecDNA to regulate unconstraint transcription, expanding the tumorigenic mechanism of HPV integration and providing insights of developing new diagnostic and therapeutic strategies.
Overall design: We employed integrative analysis on multi-omics data of cervical cancer cell lines. We performed WGS, WGBS, HiC, H3K27ac and H3K4me3 ChIP-seq, RNA-seq in 4 HPV-positive cell lines (CaSki, S12, all omics; SiHa, HeLa, except WGS), two EBV-positive cell lines (Raji, except WGBS; C666-1, except WGS and WGBS), and three non-virus cell lines (C33A, all omics; HEK293T, except WGBS and H3K4me3 ChIP-seq; HaCaT, only WGS). In addition, Raji were performed EBV virus capture sequencing and 10 normal cervical tissue from the patients were performed RNA-seq. We employed rolling-circle amplification in HeLa and S12 by long-reads sequencing, corrected by short-reads, to validate the ecDNA.
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