The Landscape of DNA Virus Associations Across Human Malignant Cancers Using RNA-Seq

Elucidation of tumor-DNA virus associations in many cancer types has enhanced our knowledge of fundamental oncogenesis mechanisms and provided a basis for cancer prevention initiatives. RNA-Seq provides a novel tool to comprehensively assess such associations.

Researchers from MD Anderson Cancer Center interrogated RNA-Seq data from 3775 malignant neoplasms in The Cancer Genome Atlas database for the presence of viral sequences. Viral integration sites were also detected in expressed transcripts using a novel approach. The detection capacity of RNA-Seq was compared to available clinical laboratory data. Human papillomavirus (HPV) transcripts were detected using RNA-Seq analysis in head and neck squamous cell carcinoma, uterine endometrioid carcinoma, and squamous cell carcinoma of the lung. Detection of HPV by RNA-Seq correlated with detection by in situ hybridization and immunohistochemistry in squamous cell carcinoma tumors of the head and neck. Hepatitis B virus and Epstein-Barr virus (EBV) were detected using RNA-Seq in hepatocellular carcinoma and gastric carcinoma tumors, respectively. Integration sites of viral genes and oncogenes were detected in cancers harboring HPV or hepatitis B virus but not in EBV-positive gastric carcinoma. Integration sites of expressed viral transcripts frequently involved known coding areas of the host genome. No DNA virus transcripts were detected in acute myeloid leukemia, cutaneous melanoma, low-and high-grade gliomas of the brain and adenocarcinomas of the breast, colon and rectum, lung, prostate, ovary, kidney and thyroid.


In conclusion, this study provides a large-scale overview of the landscape of DNA viruses in human malignant cancers. While further validation is necessary in specific cancer types, these findings highlight the utility of RNA-Seq in detecting tumor-associated DNA viruses and identifying viral integration sites that may unravel novel mechanisms of cancer pathogenesis.

  • Khoury JD, Tannir NM, Williams MD, Chen Y, Yao H, Zhang J, Thompson EJ; TCGA Network, Meric-Bernstam F, Medeiros LJ, Weinstein JN, Su X. (2013) The Landscape of DNA Virus Associations Across Human Malignant Cancers Using RNA-Seq: An Analysis of 3775 Cases. J Virol [Epub ahead of print]. [abstract]
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