A contaminant-free assessment of Endogenous Retroviral RNA in human plasma


Karamitros, Timokratis, Paraskevis, Dimitrios, Hatzakis, Angelos, Psichogiou, Mina, Elefsiniotis, Ioannis, Hurst, Tara, Geretti, Anna-Maria ORCID: 0000-0002-3670-6588, Beloukas, Apostolos ORCID: 0000-0001-5639-0528, Frater, John, Klenerman, Paul et al (show 2 more authors) (2016) A contaminant-free assessment of Endogenous Retroviral RNA in human plasma. SCIENTIFIC REPORTS, 6 (1). 33598-.

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Abstract

Endogenous retroviruses (ERVs) comprise 6-8% of the human genome. HERVs are silenced in most normal tissues, up-regulated in stem cells and in placenta but also in cancer and HIV-1 infection. Crucially, there are conflicting reports on detecting HERV RNA in non-cellular clinical samples such as plasma that suggest the study of HERV RNA can be daunting. Indeed, we find that the use of real-time PCR in a quality assured clinical laboratory setting can be sensitive to low-level proviral contamination. We developed a mathematical model for low-level contamination that allowed us to design a laboratory protocol and standard operating procedures for robust measurement of HERV RNA. We focus on one family, HERV-K HML-2 (HK2) that has been most recently active even though they invaded our ancestral genomes almost 30 millions ago. We extensively validated our experimental design on a model cell culture system showing high sensitivity and specificity, totally eliminating the proviral contamination. We then tested 236 plasma samples from patients infected with HIV-1, HCV or HBV and found them to be negative. The study of HERV RNA for human translational studies should be performed with extensively validated protocols and standard operating procedures to control the widespread low-level human DNA contamination.

Item Type: Article
Uncontrolled Keywords: Humans, Endogenous Retroviruses, HIV Infections, Deoxyribonucleases, DNA, Viral, RNA, Viral, Molecular Probes, Probability, Sensitivity and Specificity, Environment, Base Sequence, Nucleic Acid Denaturation, Genome, Models, Biological, Reference Standards, Female, Male
Depositing User: Symplectic Admin
Date Deposited: 04 Oct 2016 10:15
Last Modified: 19 Jan 2023 07:29
DOI: 10.1038/srep33598
Open Access URL: http://www.nature.com/articles/srep33598
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3003591
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