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Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer
George Washington Univ, Med Ctr, Dept Biochem & Mol Med, Washington, DC 20037 USA.
George Mason Univ, Sch Syst Biol, Manassas, VA USA.
George Washington Univ, Med Ctr, Dept Biochem & Mol Med, Washington, DC 20037 USA.
George Washington Univ, Med Ctr, Dept Biochem & Mol Med, Washington, DC 20037 USA.
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2019 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, no 4, article id e0213770Article in journal (Refereed) Published
Abstract [en]

Human endogenous retroviruses (HERVs) have been investigated for potential links with human cancer. However, the distribution of somatic nucleotide variations in HERV elements has not been explored in detail. This study aims to identify HERV elements with an over-representation of somatic mutations (hot spots) in cancer patients. Four HERV elements with mutation hotspots were identified that overlap with exons of four human protein coding genes. These hotspots were identified based on the significant over-representation (p<8.62e-4) of non-synonymous single-nucleotide variations (nsSNVs). These genes are TNN (HERV-9/LTR12), OR4K15 (HERV-IP10F/LTR10F), ZNF99 (HERV-W/HERV17/LTR17), and KIR2DL1 (MST/MaLR). In an effort to identify mutations that effect survival, all nsSNVs were further evaluated and it was found that kidney cancer patients with mutation C2270G in ZNF99 have a significantly lower survival rate (hazard ratio = 2.6) compared to those without it. Among HERV elements in the human non-protein coding regions, we found 788 HERVs with significantly elevated numbers of somatic single-nucleotide variations (SNVs) (p<1.60e-5). From this category the top three HERV elements with significantly over-represented SNVs are HERV-H/LTR7, HERV-9/LTR12 and HERV-L/MLT2. Majority of the SNVs in these 788 HERV elements are located in three DNA functional groups: long non-coding RNAs (lncRNAs) (60%), introns (22.2%) and transcriptional factor binding sites (TFBS) (14.8%). This study provides a list of mutational hotspots in HERVs, which could potentially be used as biomarkers and therapeutic targets.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE , 2019. Vol. 14, no 4, article id e0213770
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Microbiology in the medical area
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URN: urn:nbn:se:uu:diva-382521DOI: 10.1371/journal.pone.0213770ISI: 000462867000006PubMedID: 30934003OAI: oai:DiVA.org:uu-382521DiVA, id: diva2:1307983
Available from: 2019-04-30 Created: 2019-04-30 Last updated: 2019-04-30Bibliographically approved

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