Tumour virology in the era of high-throughput genomics

Tang, Ka-Wei; Larsson, Erik

doi:10.1098/rstb.2016.0265

Cited by 30 publications

(28 citation statements)

References 74 publications

(189 reference statements)

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“…Viral integration into the host genome has been shown to be a causal mechanism that can lead to cancer development 40 . This process is well-established for human papilloma viruses (HPVs) in cervical, head-and-neck and several other carcinomas, and for hepatitis B virus (HBV) in liver cancer 41,42 .…”

Section: Genomic Integration Of Viral Sequencesmentioning

confidence: 99%

The landscape of viral associations in human cancers

Zapatka

Borozan

Brewer

et al. 2018

Preprint

102

148

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Potential viral pathogens were systematically investigated in the whole-genome and transcriptome sequencing of 2,656 donors as part of the Pan-Cancer Analysis of Whole Genomes using a consensus approach integrating three independent pathogen detection pipelines. Viruses were detected in 382 genomic and 68 transcriptome data sets. We extensively searched and characterized numerous features of virus-positive cancers integrating various PCAWG datasets. We show the high prevalence of known tumor associated viruses such as EBV, HBV and several HPV types. Our systematic analysis revealed that HPV presence was significantly exclusive with well-known driver mutations in head/neck cancer. A strong association was observed between HPV infection and the APOBEC mutational signatures, suggesting the role of impaired mechanism of antiviral cellular defense as a driving force in the development of cervical, bladder and head neck carcinoma. Viral integration into the host genome was observed for HBV, HPV16, HPV18 and AAV2 and associated with a local increase in copy number variations. The recurrent viral integrations at the TERT promoter were coupled to high telomerase expression uncovering a further mechanism to activate this tumor driving process. High levels of endogenous retrovirus ERV1 expression is linked to worse survival outcome in kidney cancer.

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Section: Genomic Integration Of Viral Sequencesmentioning

confidence: 99%

The landscape of viral associations in human cancers

Zapatka

Borozan

Brewer

et al. 2018

Preprint

102

148

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show abstract

“…The decade following discovery of MCV witnessed an explosion in cancer genomic sequencing, as described by Tang and Larsson Lekholm in this issue [16], and yet no new cancer virus suspects have been uncovered. Time will tell whether we have exhausted the repertoire of human cancer viruses or if there are additional suspects that have been missed.…”

Section: (D) Viral Nucleic Acid Detectionmentioning

confidence: 99%

Human oncogenic viruses: nature and discovery

Chang

Moore

Weiss

2017

Phil. Trans. R. Soc. B

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Seven kinds of virus collectively comprise an important cause of cancer, particularly in less developed countries and for people with damaged immune systems. Discovered over the past 54 years, most of these viruses are common infections of humankind for which malignancy is a rare consequence. Various cofactors affect the complex interaction between virus and host and the likelihood of cancer emerging. Although individual human tumour viruses exert their malignant effects in different ways, there are common features that illuminate mechanisms of oncogenesis more generally, whether or not there is a viral aetiology. This article is part of the themed issue ‘Human oncogenic viruses’.

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“…Next‐generation sequencing technologies had been successfully applied to characterize the virome in various human tissues such as skin and blood 88‐90 . Traditional methods for viral detection are based on aligning short sequence reads to the reference viral genome sequences with commonly used software such as PathSequation 91 or RINs 92 .…”

Section: Discussionmentioning

confidence: 99%

Virome assembly and annotation in brain tissue based on next‐generation sequencing

Yuan

Zhu

et al. 2020

Cancer Medicine

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The glioblastoma multiforme (GBM) is one of the deadliest tumors. It has been speculated that virus plays a role in GBM but the evidences are controversy. Published researches are mainly limited to studies on the presence of human cytomegalovirus (HCMV) in GBM. No comprehensive assessment of the brain virome, the collection of viral material in the brain, based on recently sequenced data has been performed. Here, we characterized the virome from 111 GBM samples and 57 normal brain samples from eight projects in the SRA database by a tested and comprehensive assembly approach. The annotation of the assembled contigs showed that most viral sequences in the brain belong to the viral family Retroviridae. In some GBM samples, we also detected full genome sequence of a novel picornavirus recently discovered in invertebrates. Unlike previous reports, our study did not detect herpes virus such as HCMV in GBM from the data we used. However, some contigs that cannot be annotated with any known genes exhibited antibody epitopes in their sequences. These findings provide several avenues for potential cancer therapy: the newly discovered picornavirus could be a starting point to engineer novel oncolytic virus; and the exhibited antibody epitopes could be a source to explore potential drug targets for immune cancer therapy. By characterizing the virosphere in GBM and normal brain at a global level, the results from this study strengthen the link between GBM and viral infection which warrants the further investigation.

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Tumour virology in the era of high-throughput genomics

Cited by 30 publications

References 74 publications

The landscape of viral associations in human cancers

The landscape of viral associations in human cancers

Human oncogenic viruses: nature and discovery

Virome assembly and annotation in brain tissue based on next‐generation sequencing

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