This application seeks continued support for my research program, funded by the NCI for almost 40 years, with numerous innovative and high-impact contributions to the biology and evolution of retroviruses and their roles in AIDS and cancer. We will focus on a number of ongoing projects in the laboratory: 1. HERV-K (HML-2) Polymorphism in humans. HML-2 is the most recently active endogenous retrovirus group in humans, with 90 or proviruses, of which 11, all noninfectious, were known to be polymorphic in the population. To test whether active members may be present at low frequency, but remain undetected, we have developed bioinformatic and laboratory tools to identify and characterize rare - and therefore more recent and potentially infectious - proviruses in large sequence databases like those from the the ?1000 genomes? project. We have identified a number of new proviruses, rare in the population, one of which appears to be in- tact. We will determine its potential to encode infectious virus and possible role in cancer. 2. HML-2 Expression and cancer. To test for a role of HML-2 proviruses in tumor development, we have developed sequencing, bioinformatic and other tools to study their expression in cancer cell lines and deter- mine which of the 90 proviruses are expressed and by what mechanism: i.e., whether the differences in ex- pression between normal and cancer cells are due to cis (e.g., DNA methylation, chromatin structure) or trans (e.g., transcription factor patterns) effects. We will determine whether this upregulation might lead to reintegra- tion of new HML-2 proviruses, and whether it has a positive effect on tumor development and growth. 3. HML-2 expression and HIV infection. HIV-1 infected patients exhibit elevated levels of HML-2 expres- sion in PBMCs. We are developing the same approaches as in 2 to test the cell and provirus specificity of this expression in these individuals and whether it plays any role in the development of malignancy. 4. Evolution of HML-2 receptor specificity. HML-2 has been coevolving with primates for over 20 million years and has likely been subject to evolutionary forces similar to ALV. We have developed a strategy to iden- tify its host receptor based on the ability of viruses pseudotyped with HML-2 Env protein to infect cells express- ing a cDNA library from permissive cells. We will then use the ?fossil record? in primate genomes to study the coevolution of this interaction. 5. Retrovirus-APOBEC interaction. Prevention of MLV infection of human xenografts in immunodeficient mice is an issue of importance due the current interest in developing ?personalized immune? mice to grow hu- man tissues for therapeutic purposes. Our strategy is to make the recipient mice globally express a restriction factor (human APOBEC3g) that will prevent productive infection of the grafted human tumor cell line. We are also working to understand the differential sensitivity of MLV to human and murine APOBEC proteins.

Public Health Relevance

The Principal Investigator, Dr. John Coffin, has made significant contributions to understanding the biology of retroviruses, including their involvement in AIDS and cancer over nearly 40 years as an NCI-funded investigator. The goal of this proposal is to obtain extended NCI support for his research into the biology and evolution of endogenous retroviruses, whose DNA forms a large part of the human and mouse genomes, and the mechanism and impact of their frequent expression in HIV infection and cancer

National Institute of Health (NIH)
National Cancer Institute (NCI)
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Special Emphasis Panel (ZCA1)
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Read-Connole, Elizabeth Lee
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Tufts University
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Montesion, Meagan; Bhardwaj, Neeru; Williams, Zachary H et al. (2018) Mechanisms of HERV-K (HML-2) Transcription during Human Mammary Epithelial Cell Transformation. J Virol 92:
Krupovic, Mart; Blomberg, Jonas; Coffin, John M et al. (2018) Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses. J Virol 92:
Kearney, Mary F; Spindler, Jonathan; Wiegand, Ann et al. (2018) Lower pre-ART intra-participant HIV-1 pol diversity may not be associated with virologic failure in adults. PLoS One 13:e0190438
Gifford, Robert J; Blomberg, Jonas; Coffin, John M et al. (2018) Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology 15:59
Montesion, Meagan; Williams, Zachary H; Subramanian, Ravi P et al. (2018) Promoter expression of HERV-K (HML-2) provirus-derived sequences is related to LTR sequence variation and polymorphic transcription factor binding sites. Retrovirology 15:57
Van Zyl, Gert U; Katusiime, Mary Grace; Wiegand, Ann et al. (2017) No evidence of HIV replication in children on antiretroviral therapy. J Clin Invest 127:3827-3834
Coffin, John M; Fan, Hung (2016) The Discovery of Reverse Transcriptase. Annu Rev Virol 3:29-51
Wildschutte, Julia Halo; Williams, Zachary H; Montesion, Meagan et al. (2016) Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci U S A 113:E2326-34