Faculty Profile

Dr. Vinayaka R. Prasad, Ph.D.

Vinayaka R. Prasad, Ph.D.

Professor, Department of Microbiology & Immunology

Areas of Research: Development of anti-HIV RNA aptamers to modulate HIV latency and for hematopoietic stem cell therapy; Viral determinants of HIV associated neurocognitive disorders (HAND); Effect of drugs of abuse on HIV replication and HAND

Professional Interests

Research in our laboratory is focused on three areas of HIV/AIDS: HIV associated neurocognitive disorders (HAND), HIV replication mechanisms and RNA aptamers targeted to HIV.

HIV associated Neurocognitive Disorders (HAND): The severe form of HAND, the HIV associated dementia (HAD), is common among clade-B HIV-infected individuals in the US, but less common among individuals infected with clade-C HIV-1 in India, suggesting clade-specific differences in neuropathogenicity. Understanding clade-specific determinants of neuropathogenesis may shed light on the disease mechanism and help develop targeted drugs for HAD. We previously demonstrated that due to a C31S polymorphism, clade C Tat lacks the chemokine function of Clade B Tat that plays a crucial role in an increased brain infiltration of monocytic phagocytes in HAD. We studied neuropathogenesis induced by two HIV-1 clades B and C using SCID mouse HIV encephalitis (SCID-HIVE) model and reported that while the introduction of clade B HIV-1ADA into SCID mouse brain recapitulates the key features of human HAD disease, mice exposed to similar inputs of HIVIndie-C1 (clade C) made fewer memory errors than those exposed to HIV-1ADA (clade B). HIV-1ADA also caused greater astrogliosis and loss of neuronal network integrity.

Work from many groups has shown that clade C HIV-1 in Southern Africa can induce HAD at much higher incidence than in India. We hypothesized that such variation is due to polymorphism in the neuropathogenesis determinants in Tat or gp120, the two major neurotoxicity determinants of HAND. With respect to Tat, we observed that the percentage of HIV isolates with dicysteine motif in Tat is 2-3% on the Indian subcontinent while in the Southern African countries, they ranged from 19-26%. These data broadly correlate with the HAD frequencies reported from India, South Africa and Botswana (3-4%, 25% and 38% respectively). This finding has been corroborated using a Zambian HIV-1C isolate that displays a C31 residue and thus an intact dicysteine motif. Our in vitro and SCID-HIVE results clearly indicate that Tat dicysteine motif determines neurovirulence. If confirmed in population studies, it may be possible to predict neurocognitive outcomes of individuals infected with HIV-1C by genotyping Tat.

Since Tat is not the only neurovirulence determinant in HIV-1, we examined whether gp120 exhibits intra-clade differences between India and Southern Africa. Our findings indicate that gp120 can also display region-specific differences. For example, the Southern African HIV isolates appear to contain more robust neurovirulence determinants than those in the Indian isolates. Thus, two different viral genes in India appear to show determinants of low neurotoxicity. These results suggest that clinical studies studying the incidence of HAD or HAND to correlate viral genetic differences must examine both Tat and gp120. Ongoing work in our laboratory is attempting to identify the neurovirulence signatures of gp120 in clade C and clade B virus isolates and exploring the role of exosomes in neurovirulence.

Anti-HIV RNA aptamers hematopoietic gene therapy: We previously developed and tested the efficacy of novel, anti-HIV-1 RNA aptamers to inhibit HIV-1 replication. Aptamers are sequences isolated by the iterative process of SELEX and are highly specific to their targets. The most efficacious aptamers identified in our laboratory as well as combinations of them could be tested in nonhuman primates (macaques). We will introduce such aptamers into hematopoeitic stem cells, which will then be used in bone marrow transplantation followed by challenge with chimeric, pathogenic SHIVs. We have thoroughly characterized anti-RT aptamers and generated aptamers to HIV-1 Gag MA and NC proteins. Perturbation of HIV-1 Gag and viral RNA interaction using anti-Gag aptamers has provided new insights showing that preventing Gag-RNA binding causes down-modulation of viral RNA thus inhibiting virus production. Most recently, we developed high affinity aptamers (Kd = 1nM) to HIV-1 protease. We are currently characterizing the Nef aptamers to understand the specific Nef functions in HIV replication that are affected by each aptamer.

HIV Replication Mechanisms: We have a long-standing interest in elucidating the mechanistic basis of key steps in HIV-1 replication. In earlier work, we delineated the determinants of polymerase processivity, fidelity of DNA synthesis and strand displacement synthesis by HIV-1 RT. Our current work is focused on the role of beta chemokines in HIV-1 budding.

Selected Publications

HIV Neuropathogenesis

Rao, V., Neogi U, Eugenin E and Prasad, V. R. (2014) HIV-1 gp120 is a second determinant of decreased neurovirulence of Indian HIV-1C isolates compared to Southern African HIV-1C isolates. PLoS One 9(9):e107074. doi: 10.1371/journal.pone.0107074. eCollection 2014. PMCID: PMC4154767.

Rao, V., Neogi, U., Talboom, J. S., Padilla, L., Rahman, M., Fritz-French, C, Gonzalez-Ramirez, Verma, A., Wood, C., Ruprecht, R. M., Ranga, U., Azim, T., Joska, John, Eugenin, T., Shet, A., Bimonte-Nelson, Tyor, W. R. and Prasad, V. R. (2013) Clade C HIV-1 isolates circulating in Southern Africa exhibit a greater frequency of dicysteine motif-containing Tat variants than those in Southeast Asia and cause increased neurovirulence. Retrovirology 10:61. DOI: 10.1186/1742-4690-10-61.

Rao, V. R., Sas, A., Eugenin, E., Siddappa, N. B., Bimonte-Nelson, H., Berman, J., Ranga, U., Tyor, W. R. and Prasad, V. R. (2008) HIV-1 clade-specific differences in the induction of neuropathogenesis. J. Neurosci. 28:10010-6.

Dash, P. K., Siddappa, N. B., Mangaiarkarasi, A., Anand, K. K., Padmanabhan, R. B, Mahendarkar, A. V., Mahadevan, A., Satishchandra, P., Shankar, S. K., Prasad, V. R., Ranga, U. (2008) Expanded coreceptor use of Human Immunodeficiency Virus Type-1 subtype C molecular isolates from an Indian subject with HIV-1 associated dementia. Retrovirology 5:25

Ranga, U., Shankarappa, R., Siddappa, N. B., Lakshmi, R., Nagendran, R., Mahalingam, M., Mahadevan, A., Jayasuryan, N., Satishchandra, P., Shankar, S.K. and Prasad, V. R. (2004)Tat protein of HIV-1subtype-C viruses is a defective chemokine. J. Virol. 78:2586-2590.

RNA aptamers targeted to HIV-1

Duclair, S., Gautam, A., Ellington, A. and Prasad, V. R. (2014) High affinity RNA aptamers against HIV-1 protease inhibit both in vitro protease activity and late events of viral replication. Mol. Ther. Nuc. Acids. 4:e228. doi: 10.1038/mtna.2015.1.

Ramalingam, D, Duclair, S., Datta, S., Ellington, A.D., Rein, A. and Prasad, V. R. (2010) RNA aptamers directed to HIV-1 Gag bind to the matrix and nucleocapsid domains and inhibit virus production. J. Virol. 85:305-314.

Joshi. P., North, T. W. and Prasad, V. R. (2005) Aptamers Directed to HIV-1 Reverse Transcriptase Display Greater Efficacy over Small Hairpin RNAs Targeted to Viral RNA in Blocking HIV-1 Replication. Mol. Ther. 11:677-686.

HIV-1 Replication Mechanisms

Lwatula, C., Garforth, SJ and Prasad, VR (2012) Lys66 as a determinant of high mismatch extension and misinsertion rates of HIV-1 reverse transcriptase FEBS J 2012 Aug 28. doi:10.1111/j.1742-4568.2012.08807.x.[Epub ahead of print]

Garforth, S. J., Domaoal, R. A., Lwatula, C., Landau, M. J., Meyer, A. J., Anderson, K. S. and Vinayaka Prasad (2010) K65R and K65A substitutions in HIV-1 reverse transcriptase enhance polymerase fidelity by decreasing both dNTP misinsertion and mispaired primer extension efficiencies. J. Mol. Biol. 401:33-44.

Garforth, S.,Parniak, M. A. and Prasad, V. R. (2008) Utilization of deoxynucleoside diphosphates as substrate by a DNA polymerase. Plos One. 3(4):e2074.

Garforth, S., Lee, T. W., Parniak, M. A., Kool, E. T. and Prasad, V. R. (2007) Site-directed mutagenesis in the fingers subdomain of HIV-1 reverse transcriptase reveals a specific role for the b3- b4 hairpin loop in dNTP selection. J. Mol. Biol. 365:38-49





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