David N. Levy, PhD

Associate Professor
New York University College of Dentistry
921 Schwartz Building
345 East 24th Street
New York, NY 10010
Phone: 212-998-9287
Fax: 212-995-3250
E-mail:

Education

PhD, Immunology, University of Pennsylvania, Philadelphia, PA 1994
BA, Biology, Williams College, Williamstown, MA 1985

Research Interests / Professional Overview

My laboratory studies the replication, pathogenesis and immunology of the human immunodeficiency virus (HIV). In prior years I pioneered study of HIV-1 recombination, Vpr (1)(2), the development of widely utilized and distributed research tools, including reporter viruses and latently infected cell lines that enable direct single cell analysis of HIV replication, latency and pathogenesis. Currently, we combine in vitro, ex vivo and in vivo approaches to study viral dynamics and novel replication mechanisms (1)(2)(3) and regulatory pathways that we have discovered. I have been NIH R01 funded since 2004.

HIV suppression of the transcription factor Foxo1.  The low metabolic activity of resting CD4 T cells presents an obstacle that is partially met by the ability of HIV to increase their activation state. This is achieved through the combined effects of Env, Tat and Nef on cell signaling cascades, particularly PI3K/Akt.  We recently reported  that HIV-1 infection of resting CD4+ T cells results in the suppression of the activity of Foxo1, a transcription factor that regulates many processes in resting T cells, including maintenance of T cell quiescence, migration, survival and differentiation. We found that suppression of Foxo1 activity involves PI3K/Akt activation, which results in Foxo1 phosphorylation and inactivation. HIV-1 suppression of Foxo1 down modulates CD62L (L-selectin), a cell surface receptor that is required for T cell migration in to lymph nodes as well as a series of genes regulating many aspects of T cell immunobiology. These findings have broad ramifications for how HIV replicates and causes disease. Foxo1 is implicated in several cancers and metabolic disorders, is a target for drug development, and we believe that the manipulation of Foxo1 by these approaches may have utility in treating HIV infection. For example, we find that inhibitors of the kinase Akt specifically kill HIV-1 infected resting T cells, while leaving uninfected cells intact. A Foxo1 inhibitor enhances infected cell survival and virus output, providing evidence that Foxo1 is the major downstream effector. We are actively investigating the molecular mechanism of HIV suppression of Foxo1, how this affects virus replication, and how intervention in the HIV/Foxo1 nexus may be therapeutically useful. These studies are being conducted in part through a collaboration with Dr. Elizabeth Connick, U. Colorado, Denver.

Novel replication pathways utilizing unintegrated HIV genomes.   As a member of the retrovirus family, HIV integrates its DNA into cells' chromosomal DNA. However, this integration process is prone to failure, resulting in the accumulation of a great excess of unintegrated HIV genomes. This unintegrated DNA (uDNA) has been considered a dead end waste product without relevance to the natural history of HIV. We have established that uDNA is in fact a competent template for de novo virus production through two important mechanisms:

We recently demonstrated  that HIV generates a large amount of stable uDNA in resting CD4 T cells that produces infectious virions when T cell activation follows infection. This does not occur when T cell activation precedes infection, as the replication of the cells dilutes the uDNA and its gene products below the level that supports de novo virus production. We demonstrated that uDNA establishes a stable reservoir of latent genomes in resting CD4+ T cells from which virus production can be recruited by T cell activation many weeks after infection.  We are investigating the response of uDNA  (PKC agonists, histone deacetylase inhibitors, P-TEFb agonists, etc.) that are under investigation as potential curative therapies. We have found that inhibiting HIV-1 integration enhances the production of latently infected cells by shunting viral genomes to the less cytopathic unintegrated pathway of replication. Models of HIV latency which utilize direct infection of resting CD4+ cells must accommodate these findings. Finally, we find that unintegrated HIV is unable to down modulate MHC Class I, a function of the Nef protein that helps HIV evade cellular immunity. We further find HIV-specific cytotoxic T cells efficiently kill cells expressing HIV proteins from unintegrated HIV-1 – in collaboration with Dr. Paul Goepfert at the University of Alabama at Birmingham (manuscript in preparation).

In the second replication pathway when more than one HIV virion infect the same cell, a uDNA genome is frequently co-resident with an integrated provirus. In this multiple infection mechanism, the integrated provirus provides factors that complement the uDNA genome, enabling it to generate genomic RNA that is packaged into virions produced by the integrated provirus. This enables uDNA to enhance the number of replicating genomes that contribute to viral diversity and genetic recombination.

Vpr.   Vpr is a small HIV protein that is incorporated into virions and performs several functions, including cell cycle arrest and transactivation. We also demonstrated  that the HIV-1 Vpr protein must be delivered into infected cells at the time of infection in order for the unintegrated HIV DNA to be competent for viral expression. We are investigating the molecular pathways by which Vpr, a known transactivator and a chromatin-associated protein, enables gene expression from uDNA.

HIV-1 replication dynamics.   Our research facilitate quantitative single cell analysis of HIV-1 evolution and replication, and data generated by my laboratory and many others has been fundamentally important to our understanding of HIV dynamics. For example, HIV multiple infection of cells has many consequences, including genetic recombination, virus complementation, virus competition, increased cytopathicity and increased virus production. Using a variety of cellular, molecular and immunological techniques,  we are examining  these processes. In collaboration with  Dr. Dominik Wodarz, University of California, Irvine,  we are applying the knowledge gained from our laboratory experiments to the development of quantitative models of HIV replication and pathogenesis. We are funded for this work by a 4 year NIH/NIAID R01 grant.

Link to Levy/Wodarz Articles in PubMed


I am the Director of the NYUCD Flow Cytometry Core Facility.


Lab Personnel:

  • Benjamin Trinite, Ph.D., Post Doctoral Fellow
  • Chi Chan, Ph.D, Post Doctoral Fellow
  • Caroline Lee, Lab Assistant
  • Akanksha Ananad, NYU Polytechnic student assistant

  • My Linkedin page


    Current Funding

    HIV-1 Replication without integration. NIH/NIAID R01 AI078783

    Virus Dynamics and Multiple Infection of Cells: Computational and Experimental Analysis. NIH/NIAID/NIGMS R01 AI093998


    Representative Publications


    Search PubMed for articles "Levy DN".

    Haas, M. K., Levy, D. N., Folkvord, J. M., Connick, E. Distinct Patterns of Bcl-2 Expression Occur in R5- and X4-tropic HIV-1-Producing Lymphoid Tissue Cells Infected Ex vivo. Aids Research and Human Retroviruses. ePub ahead of print Oct 29, 2014.

    Trinite, B., Chan, C. N., Mahajan, S., Luo, Y., Muesing, M. A., Folkvord, J. M., Pham, M., Connick, E. and D. N. Levy. (2014). Suppression of Foxo1 activity and down-modulation of CD62L (L-selectin) in HIV 1 infected resting CD4 T cells. PLoS One. 9(10):e110719.

    Lau J. W., Levy D. N. , Wodarz D. Contribution of HIV-1 genomes that do not integrate to the basic reproductive ratio of the virus. J Theor Biol. 2014. J Theor Biol. 367C:222-229.

    Wodarz, D., Chan, C.N., Trinite, B., Komarova, N.L., and D. N. Levy. (2014). On the laws of virus spread through cell populations. Journal of Virology. J Virol 88: 13240-13248.

    Weiden, M., Hoshino, S., Kimura T., Li, Y., Levy, D. N., Burke, S. A., Borkowsky, W., Rom, W.N., and Y. Hoshino. Interferon-γ Induces Adenosine Deaminase acting on RNA-1 (ADAR1) to inhibit HIV-1 Replication in Human Macrophages. PLoS One. 9(10):e108476.

    Trinite, B., Ohlson, E.C., Voznesensky, I., Rana, S. P., Chan, C.N., Mahajan, S., Alster, J., Burke, S. A., Wodarz, D., and D. N. Levy. (2013). An HIV 1 replication pathway utilizing reverse transcript products that fail to integrate. Journal of Virology. 87:12701-20.

    Komarova, N. L., Levy, D. N. and D. Wodarz. (2013). Synaptic transmission and the susceptibility of HIV infection to anti-viral drugs. Sci. Rep. 3:2103

    Komarova, N. L., Anghelina, D., Voznesensky, I., Trinite, B., Levy, D. N. and D. Wodarz. (2013). Relative contribution of free virus and synaptic transmission to the spread of HIV through target cell populations. Biol. Letters. 9:20121049.

    Komarova, N. L., Levy, D. N. and D. Wodarz. (2012). Effect of synaptic transmission on viral fitness in HIV infection. PLoS One. 7(11):e48361.

    Cummings, K. W., Levy, D. N. D. Wodarz. (2012). Increased burst size in multiply infected cells alters basic infection dynamics. Biology Direct. 7:16.

    Meditz, A. L., Haas, M. K., Folkvord, J. M., Melander, K., Young, R., McCarter, M., MaWhinney, S., Campbell, T., Weinberg, A., Coakley, E., Levy, D. N., E. Connick. (2011). HLA-DR+CD38+ T Lymphocytes Express High Levels of CCR5 and Produce the Majority of R5-tropic HIV-1 in Human Lymph Nodes. Journal of Virology. J Virol. 85:10189-200

    Wodarz, D. and D. N. Levy. (2011). Effect of multiple infection of cells on the evolutionary dynamics of HIV in vivo: implications for host adaptation mechanisms. Experimental Biology and Medicine. 236: 926-937.

    Del Portillo, A., Tripodi, J., Najfeld, V., Wodarz, D., D. N. Levy. , B. K. Chen. (2011). Multiploid inheritance of HIV-1 during cell-to-cell infection. Journal of Virology, 85:7169-7176.

    Wodarz, D. and D. N. Levy. (2010). Effect of different modes of viral spread on the dynamics of multiply infected cells in human immunodeficiency virus infection. Journal of the Royal Society Interface. 8:289-300.

    Bansal, A., Carlson, J., Yan, J., Olusimidele, T. A., Schaefer, M., Sabbaj, S., Bet, A., Levy, D. N., Heath, S., Walker, B. D., Ndung'u, T., Goulder, P. J., Heckerman, D., Hunter, E., P. A. Goepfert. (2010). CTL response and evolutionary changes to HIV-1 cryptic epitopes derived from antisense transcription. J. Exp. Med. 207:51-59.

    Hioe, C., Visciano, M. L., Kuman, R., Liu, J., Levy, D. N., Tuen, M. (2009). The use of immune complex vaccines to enhance antibody response against neutralizing epitopes on HIV-1 envelope gp120. Vaccine. 28:352-360.

    Wodarz, D. and D. N. Levy. (2009). Multiple infection of cells and the evolutionary dynamics of cytotoxic T lymphocyte escape mutants. Evolution. 63:2326-2339.

    Gelderblom, H. C., , Vatakis, D., Burke, S. A., Lawrie, S., Bristol, G. A., D. N. Levy. (2008). Viral complementation allows HIV-1 replication without integration. Retrovirology. 5:60.

    Commentary on Gelderblom et al. in Retrovirology.

    Wodarz, D. and D. N. Levy. (2007). HIV coinfection and viral evolution towards reduced replicative fitness: a requirement for the development of AIDS? Proc. Royal Soc. B. 274:2481-2490.

    Decker, J. M., Bibollet-Ruche, F., Wei, X., Wang, S., Levy, D. N., Derdeyn, C. A., Allen, S., Hunter, E., Saag, M. S., Hoxie, J., Hahn, B. H., Kwong, P. D., Robinson, J. E., and G. M. Shaw. (2005). Antigenic Conservation and Immunogenicity of the HIV Co-Receptor Binding Site. J. Exp. Med. 201:1407-1419.

    Kutsch, O., Levy, D. N., Bates, P. J., Decker, J., Kosloff, B. R., Shaw, G. M., Priebe, W., and E. N. Benveniste. (2004). Bis-anthracycline antibiotics target HIV-1 tat transactivation. Antimicrob. Agents Chemother. 48:1652-1663.

    Levy, D. N., Aldrovandi, G. M., Kutsch, O., and G. M. Shaw. (2004). Dynamics of HIV-1 recombination in its natural target cells. Proc. Natl. Acad. Sci. USA. 101:4204-4209.

    Click to view Journal Cover

    Gao, F., Chen, Y., Levy, D. N., Conway, J. A., Kepler, T. B., and H. Hui. (2004). Unselected mutations in the human immunodeficiency virus type 1 genome are mostly non-synonymous and often deleterious. J. Virol. 78:2426-2433.

    Kutsch, O., Levy, D. N., Kosloff, B. R., Shaw, G. M., and E. N. Beneveniste. (2003).
    CD154-CD40 induced reactivation of latent HIV-1. Virology. 314:261-270.

    Kutsch, O., Beneveniste, E. N., Shaw, G. M., and D. N. Levy. (2002). Direct and quantitative single-cell analysis of human immunodeficiency virus type 1 reactivation from latency. J. Virol. 76:8776-8786.

    Agadjanyan, M. G., Trivedi, N. N., Kudchodkar, S., Bennet, M., Levine, W., Lin, A., Boyer, J., Levy, D., Ugen, K. E., Kim, J. J., and Weiner, D. B. (1997). An HIV type 2 DNA vaccine induces cross-reactive immune responses against HIV type 2 and SIV. AIDS Res. Hum. Retroviruses. 13:1561-1572.

    Refaeli, Y., Levy, D. N., and Weiner, D. B. (1995). The glucocorticoid receptor type II complex is a target of the HIV-1 vpr gene product. Proc. Natl. Acad. Sci. USA. 92:321-3625.

    Levy, D. N., Refaeli, Y., and Weiner, D. B. (1995). Extracellular vpr protein increases cellular permissiveness to human immunodeficiency virus type 1 replication and reactivates virus from latency. J. Virol. 69:1243-1252.

    Levy, D. N., Refaeli, Y., and Weiner, D. B. (1994). Serum vpr regulates productive infection and latency of human immunodeficiency virus type 1. Proc. Natl. Acad. Sci. USA. 91:10873-10877.

    Levy, D. N., Fernandes, L. S., Williams, W. V., and Weiner, D. B. (1993). Induction of cell differentiation by human immunodeficiency virus 1 vpr. Cell. 72:541-550.

    Click to view Journal Cover

     

    Book Chapters:

    Levy, D. N., Refaeli, Y., and Weiner, D. B. (1995). The vpr regulatory gene of HIV. In: Transacting functions of human retroviruses; Current Topics in Microbiology and Immunology. Vol 193. pp. 209-236. Springer-Verlag, Berlin. Chen, I.S.Y, Koprowski, H., Srinivasan, A, and Vogt. P.A., eds.

    Levy, D. N. and Weiner, D. B. (1993). HIV-1 regulatory gene function analysis in a rhabdomyosarcoma cell line. pp. 243-249. Vaccines93, Modern Approaches to New Vaccines Including the Prevention of AIDS. Cold Spring Harbor Laboratory Press. Cold Spring Harbor, New York, N.Y.

    Levy, D. N. and Weiner, D. B. (1993). Synthetic peptide-based vaccines and antiviral agents including HIV/AIDS as a model system. pp. 219-267. Biologically Active Peptides: Design, Synthesis, and Utilization. Williams, W.V. and Weiner, D.B., Eds. Technomic Publishing Company, Malvern, PA.