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Article

Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival

1
Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA
2
Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
3
Department of Medicine, The University of Chicago Medicine, Chicago, IL 60637, USA
4
Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10021, USA
5
Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA
6
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(9), 956; https://doi.org/10.3390/v12090956
Received: 30 June 2020 / Revised: 12 August 2020 / Accepted: 26 August 2020 / Published: 28 August 2020
(This article belongs to the Special Issue Endogenous Retroviruses in Development and Disease)
Human endogenous retroviruses (HERVs) have been implicated in a variety of human diseases including cancers. However, technical challenges in analyzing HERV sequence data have limited locus-specific characterization of HERV expression. Here, we use the software Telescope (developed to identify expressed transposable elements from metatranscriptomic data) on 43 paired tumor and adjacent normal tissue samples from The Cancer Genome Atlas Program to produce the first locus-specific retrotranscriptome of head and neck cancer. Telescope identified over 3000 expressed HERVs in tumor and adjacent normal tissue, and 1078 HERVs were differentially expressed between the two tissue types. The majority of differentially expressed HERVs were expressed at a higher level in tumor tissue. Differentially expressed HERVs were enriched in members of the HERVH family. Hierarchical clustering based on HERV expression in tumor-adjacent normal tissue resulted in two distinct clusters with significantly different survival probability. Together, these results highlight the importance of future work on the role of HERVs across a range of cancers. View Full-Text
Keywords: RNA-seq; transposable element; endogenous retrovirus; cancer; TCGA RNA-seq; transposable element; endogenous retrovirus; cancer; TCGA
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MDPI and ACS Style

Kolbe, A.R.; Bendall, M.L.; Pearson, A.T.; Paul, D.; Nixon, D.F.; Pérez-Losada, M.; Crandall, K.A. Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival. Viruses 2020, 12, 956. https://doi.org/10.3390/v12090956

AMA Style

Kolbe AR, Bendall ML, Pearson AT, Paul D, Nixon DF, Pérez-Losada M, Crandall KA. Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival. Viruses. 2020; 12(9):956. https://doi.org/10.3390/v12090956

Chicago/Turabian Style

Kolbe, Allison R., Matthew L. Bendall, Alexander T. Pearson, Doru Paul, Douglas F. Nixon, Marcos Pérez-Losada, and Keith A. Crandall. 2020. "Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival" Viruses 12, no. 9: 956. https://doi.org/10.3390/v12090956

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