Human papilloma virus integration sites and genomic signatures in head and neck squamous cell carcinoma

Abstract

A prevalence of around 26% of human papillomavirus (HPV) in head and neck squamous cell carcinoma (HNSCC) has been previously reported. HPV induced oncogenesis mainly involving E6 and E7 viral oncoproteins. In some cases, HPV viral DNA has been detected to integrate with the host genome and possibly contributes to carcinogenesis by affecting the gene expression. We retrospectively assessed HPV integration sites and signatures in 80 HPV positive patients with HNSCC, by using a double capture‐HPV method followed by next‐generation Sequencing. We detected HPV16 in 90% of the analyzed cohort and confirmed five previously described mechanistic signatures of HPV integration [episomal (EPI), integrated in a truncated form revealing two HPV‐chromosomal junctions colinear (2J‐COL) or nonlinear (2J‐NL), multiple hybrid junctions clustering in a single chromosomal region (MJ‐CL) or scattered over different chromosomal regions (MJ‐SC) of the human genome]. Our results suggested that HPV remained episomal in 38.8% of the cases or was integrated/mixed in the remaining 61.2% of patients with HNSCC. We showed a lack of association of HPV genomic signatures to tumour and patient characteristics, as well as patient survival. Similar to other HPV associated cancers, low HPV copy number was associated with worse prognosis. We identified 267 HPV‐human junctions scattered on most chromosomes. Remarkably, we observed four recurrent integration regions: PDL1/PDL2/PLGRKT (8.2%), MYC/PVT1 (6.1%), MACROD2 (4.1%) and KLF5/KLF12 regions (4.1%). We detected the overexpression of PDL1 and MYC upon integration by gene expression analysis. In conclusion, we identified recurrent targeting of several cancer genes such as PDL1 and MYC upon HPV integration, suggesting a role of altered gene expression by HPV integration during HNSCC carcinogenesis.

Human papillomavirus (HPV) integration signature in cervical lesions: identification of MACROD2 gene as HPV hot spot integration site

“…Consistently, Kamal et al found that patients with HPV integration sites into the MACROD2 gene (introns 5, 6 and 7) [14]. Juliette Mainguené et al reported that the third HPV integration hotspot is MACROD2 (4.1%) in head and neck squamous cell carcinoma, with two patients displaying intragenic HPV integration [24]. MACROD2 is a protein-coding gene located at a fragile site on human chromosome 20.…”

Direct Comparison of HPV16 Viral Genomic Integration, Copy Loss, and Structural Variants in Oropharyngeal and Uterine Cervical Cancers Reveal Distinct Relationships to E2 Disruption and Somatic Alteration

“…The ability of HPV integration to alter expression of nearby human genes (within 500 Kb) has been demonstrated in both OPSCC and UCSCC [ 7 , 12 ] with recurrent integration sites identified near genes implicated in cancer such as MYC [ 7 , 50 ], MYB [ 7 ], PVT1 [ 51 , 52 , 53 ], RAD51B [ 50 , 54 ], EMBP1 [ 55 ], CD274/PD-L1 [ 7 , 56 ], and SOX2 [ 7 ]. Our results agree with these prior reports confirming integration in or near these genes.…”

HPV Integration Site Mapping: A Rapid Method of Viral Integration Site (VIS) Analysis and Visualization Using Automated Workflows in CLC Microbial Genomics

“…Of note, differences in search parameters (e.g., 100 vs. 500 KB for nearby gene distance) accounted for expected discrepant results. As mentioned in the Section 1 , developer-based workflows have also been reported for the advancement of viral integration site analysis [ 23 , 24 ]. However, the drawbacks of command-line based, open-source software must be deliberated.…”

“…Contrarily, the accompanying bioinformatics analysis has been lagging in development and implementation. Both manual and developer-based, viral-host mapping workflows, i.e., SearcHPV, and nf-VIF (nextflow-based Virus Insertion Finder) have been reported [ 22 , 23 , 24 ]. However, drawbacks of open-source software must be considered by the inexpert user to include: (1) prerequisite for advanced computational skills, (2) uncertainty of software maintenance and support (“abandonware”), (3) security risk, and (4) prohibition by some governmental institutions [ 25 , 26 , 27 ].…”