The functions of the approximately 98% of the human genome that do not encode human cellular proteins remain to be elucidated. Actively replicating endogenous retroviruses entered the human genome millions of years ago and became a stable part of the inherited genetic material, with retroviral elements presently making up approximately 8% of the modern human genome. These viruses subsequently acquired multiple mutations, leading to the widely-held assumption that they are no longer competent to replicate. However, in studying living patients rather than the standard cell lines, we have recently discovered surprising evidence suggesting that in certain patients with cancer HERV-K (HML-2), an endogenous retrovirus that is a relatively recent entrant into the human genome and has been linked to oncogenesis, might still be capable of replication. Replication and transmission of endogenous retroviruses is difficult to prove using standard techniques, however, as these viruses are already present in the genomes of all human cells. Therefore, we have assembled a diverse and expert group of investigators who will test the hypothesis that modern HERV-K (HML-2) can replicate using cutting-edge and complementary techniques. We will use a newly devised molecular system in which antibiotic resistance serves as a surrogate marker to assess whether we can passage virus from the blood of patients in the laboratory. We will also use high-throughput DNA sequencing and Bioinformatics to find full-length functional virus that is present in cancer patients but is not represented in the current draft of the human genome. An infectious clone that is representative of modern HERV-K (HML-2) will be made by using the information gained from the Bioinformatics studies and/or by cloning a full-length virus from the HERV-K RNA found in the blood of patients. This clone will then be tagged with green fluorescent protein and used to directly study replication. Building on our advances using Nuclear Magnetic Resonance (NMR) to visualize spatially correlated dynamics that direct RNA and protein conformational transitions, we will also develop NMR methods to visualize HERV-K (HML-2) replication in vivo. Proof that endogenous retroviruses can still replicate in modern humans will lead to a paradigm shift in thinking about these viruses, and will suggest a role for them in reshaping individual genomes. In addition, as increased expression of chromosomal endogenous retroviral sequences has been linked to cancer and autoimmunity, these findings will be relevant to understanding the pathogenesis of significant diseases. Finally, if replicating, infectious endogenous human retroviruses capable of causing disease can be found in the blood of given individuals, this information will have important implications for the safety of the blood supply.

Public Health Relevance

Here we propose to prove that, contrary to the entrenched dogma, certain human endogenous retroviruses can still replicate in modern humans. Proof of this hypothesis would have substantial implications for human genetics, cancer biology, and the safety of the human blood supply.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA144043-04
Application #
8318290
Study Section
Special Emphasis Panel (ZRG1-BCMB-A (51))
Program Officer
Read-Connole, Elizabeth Lee
Project Start
2009-09-28
Project End
2014-08-31
Budget Start
2012-09-01
Budget End
2013-08-31
Support Year
4
Fiscal Year
2012
Total Cost
$1,231,806
Indirect Cost
$430,369
Name
University of Michigan Ann Arbor
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
073133571
City
Ann Arbor
State
MI
Country
United States
Zip Code
48109
Gonzalez-Hernandez, Marta J; Cavalcoli, James D; Sartor, Maureen A et al. (2014) Regulation of the human endogenous retrovirus K (HML-2) transcriptome by the HIV-1 Tat protein. J Virol 88:8924-35
Menon, Rajasree; Im, Hogune; Zhang, Emma Yue et al. (2014) Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. J Proteome Res 13:212-27
Dube, Derek; Contreras-Galindo, Rafael; He, Shirley et al. (2014) Genomic flexibility of human endogenous retrovirus type K. J Virol 88:9673-82
Lane, Lydie; Bairoch, Amos; Beavis, Ronald C et al. (2014) Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res 13:15-20
Omenn, Gilbert S; Guan, Yuanfang; Menon, Rajasree (2014) A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines. J Proteomics 107:103-12
Markovitz, David M (2014) "Reverse genomics" and human endogenous retroviruses. Trans Am Clin Climatol Assoc 125:57-62; discussion 62-3
Omenn, Gilbert S (2014) The strategy, organization, and progress of the HUPO Human Proteome Project. J Proteomics 100:3-7
Omenn, Gilbert S; Menon, Rajasree; Zhang, Yang (2013) Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. J Proteomics 90:28-37
Contreras-Galindo, Rafael; Kaplan, Mark H; He, Shirley et al. (2013) HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses. Genome Res 23:1505-13
Contreras-Galindo, Rafael; Kaplan, Mark H; Contreras-Galindo, Angie C et al. (2012) Characterization of human endogenous retroviral elements in the blood of HIV-1-infected individuals. J Virol 86:262-76

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