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Retroviruses are RNA viruses that have been shown to cause cancers in diverse species, including chickens, mice, cats, and monkeys. The RNA genomes of these viruses are first reverse-transcribed into single and then double-stranded DNA (dsDNA) copies. This dsDNA called proviral DNA then integrates into the host genome. Subsequently, the host cell transcribes the proviral DNA in concert with the chromosomal DNA. This leads to the production of viral RNA and proteins that assemble at the host...
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Viral sequences in human cancer.

Paul G Cantalupo1, Joshua P Katz1, James M Pipas1

  • 1Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.

Virology
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PubMed
Summary

A new computational pipeline, Pickaxe, identified viral sequences in The Cancer Genome Atlas (TCGA) data. Herpesviruses were found across multiple cancers, with Human papillomaviruses (HPV) linked to bladder cancer tumorigenesis.

Keywords:
CancerHerpesvirusMetagenomicsPapillomavirusTCGAVirome

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Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer
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Area of Science:

  • Oncology
  • Virology
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) data frequently contains viral sequences.
  • Identifying and characterizing these viral contaminants is crucial for accurate cancer genomics research.

Purpose of the Study:

  • To develop and apply a computational pipeline (Pickaxe) for virus detection and discovery in The Cancer Genome Atlas (TCGA) database.
  • To investigate the prevalence and types of viral infections across various cancer types using whole genome, exome, and RNA sequencing data.

Main Methods:

  • Utilized the Pickaxe pipeline on NGS data from 3052 participants across 22 cancer types.
  • Analyzed whole genome (WGS), exome (WXS), and RNA sequencing (RNA-Seq) libraries.
  • Performed computational and manual curation to identify and remove viral sequence artifacts.

Main Results:

  • Viral sequences were detected in NGS data from nearly all tumor and normal tissues examined.
  • Herpesviruses (EBV, CMV, HHV1-7) were identified in several cancer types.
  • Human papillomaviruses (HPV) were found in cervical, head and neck, and additionally in a subset of bladder cancers.
  • Evidence suggests HPV integration drives tumorigenesis in these bladder cancer cases.

Conclusions:

  • The Pickaxe pipeline effectively detects viral sequences in large-scale cancer genomics datasets.
  • Viral infections, including Herpesviruses and HPV, are prevalent across diverse cancer types.
  • HPV may play a direct role in the oncogenesis of a subset of bladder cancers.