The landscape of viral associations in human cancers.
journal contributionposted on 2023-07-17, 12:54 authored by Marc Zapatka, Ivan Borozan, Daniel S Brewer, Murat Iskar, Adam Grundhoff, Malik Alawi, Nikita Desai, Holger Sültmann, Holger Moch, PCAWG Pathogens, Colin S Cooper, Roland Eils, Vincent Ferretti, Peter Lichter, PCAWG Consortium
Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and-for a subset-whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using a consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets. We found a high prevalence of known tumor-associated viruses such as Epstein-Barr virus (EBV), hepatitis B virus (HBV) and human papilloma virus (HPV; for example, HPV16 or HPV18). The study revealed significant exclusivity of HPV and driver mutations in head-and-neck cancer and the association of HPV with APOBEC mutational signatures, which suggests that impaired antiviral defense is a driving force in cervical, bladder and head-and-neck carcinoma. For HBV, HPV16, HPV18 and adeno-associated virus-2 (AAV2), viral integration was associated with local variations in genomic copy numbers. Integrations at the TERT promoter were associated with high telomerase expression evidently activating this tumor-driving process. High levels of endogenous retrovirus (ERV1) expression were linked to a worse survival outcome in patients with kidney cancer.
DNA Copy Number VariationsDNA Tumor VirusesGenome, HumanHepatitis B virusHerpesvirus 4, HumanHumansMutationNeoplasmsPapillomavirus InfectionsPromoter Regions, GeneticTelomeraseTranscriptomeTumor Virus InfectionsVirus IntegrationPCAWG PathogensPCAWG ConsortiumVan Loo FC001202Jones - sec06 Biological Sciences11 Medical and Health SciencesDevelopmental Biology