Intratumoral heterogeneity and clonal evolution induced by HPV integration

Abstract

The human papillomavirus (HPV) genome is integrated into host DNA in most HPV-positive cancers, but the consequences for chromosomal integrity are unknown. Continuous long-read sequencing of oropharyngeal cancers and cancer cell lines revealed interrelated but heterogeneous genomic structures comprising repetitive patterns of concatemerized virus and host segments. Evidence of this novel form of structural variation -- termed "circacatena" here -- was detected in extrachromosomal and intrachromosomal DNA and at chromosomal rearrangements. Unique breakpoint sequences shared across structurally diverse virus-host concatemers facilitated stepwise reconstruction of their evolution from common molecular ancestors. This analysis revealed that concatemerized HPV genomes are unstable and, upon insertion into and excision from chromosomes, facilitate capture, rearrangement, and rolling-circle amplification of host DNA. The data indicate that circacatena is driven by the dynamic, aberrant replication and recombination of an oncogenic DNA virus, thereby extending known consequences of HPV integration to include promotion of intratumoral heterogeneity and clonal evolution.

Long-read sequencing of oropharyngeal squamous cell carcinoma tumors reveal diverse patterns of high-risk Human Papillomavirus integration

“…They identified a new type of genomic structural variation, named "heterocateny", described as heterogeneous, interrelated, and repetitive patterns of integrated and concatemerized virus and host DNA segments (30). According to this study, "heterocateny" would contribute to chromosomal instability and rearrangement and promote tumorigenesis in OPSCCs (30). All three studies helped deepen our understanding of oncogenic mechanisms behind persistent hrHPV infection.…”

“…However, in 2023, Akagi et al performed long-read sequencing on five HPV positive OPSCC patient tumors. They identified a new type of genomic structural variation, named "heterocateny", described as heterogeneous, interrelated, and repetitive patterns of integrated and concatemerized virus and host DNA segments (30). According to this study, "heterocateny" would contribute to chromosomal instability and rearrangement and promote tumorigenesis in OPSCCs (30).…”

“…In recent years, Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) released their long-read sequencing platforms. Oxford Nanopore long-read sequencing technology allows reads of up to 1 Mb in a single read with an average of 5-15 kb per read while PacBio allows reads of up to 70 kb in a single read (30)(31)(32). We chose Oxford Nanopore long read sequencing as they can produce reads up to 1 Mb to detect all types of HPV integration events.…”

AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes

“…AA then explores the genome graph to decompose it into paths and cycles, constrained by the copy-number available. For focal amplifications of simple structure, individual decompositions may capture the full structure of the focal amplification, but in complex cases they typically represent substructures of a larger or more heterogeneous amplicon 21,22 . To improve the quality of results, AmpliconSuite-pipeline automatically detects samples with poorly controlled insert size distribution, where library preparation resulted in a high rate of read pairs marked as discordant (properly paired rate < 90%) and adjusts AA's parameters accordingly, reducing falsepositive SV calls (Supplementary Figure 2).…”