The landscape of viral associations in human cancers

Marc Zapatka, Ivan Borozan, Daniel S Brewer, Murat Iskar, Adam Grundhoff, Malik Alawi, Nikita Desai, Holger Sültmann, Holger Moch, Colin S Cooper, Roland Eils, Vincent Ferretti, Peter Lichter, Åke Borg (Contributor), Markus Ringnér (Contributor), Johan Staaf (Contributor), PCAWG Pathogens, PCAWG Consortium

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)320-330
JournalNature Genetics
Volume52
Issue number3
DOIs
Publication statusPublished - 2020 Mar

Subject classification (UKÄ)

  • Medical Genetics

Free keywords

  • DNA Copy Number Variations
  • DNA Tumor Viruses/genetics
  • Genome, Human/genetics
  • Hepatitis B virus/genetics
  • Herpesvirus 4, Human/genetics
  • Humans
  • Mutation
  • Neoplasms/genetics
  • Papillomavirus Infections/genetics
  • Promoter Regions, Genetic/genetics
  • Telomerase/genetics
  • Transcriptome
  • Tumor Virus Infections/virology
  • Virus Integration

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