Vinay K. Pathak, Ph.D.
Dr. Pathak has significantly advanced the field of lentiviral molecular virology with his studies of the mechanisms by which retroviruses replicate in the presence of potent host defense mechanisms and antiviral drugs. Under his direction, the Viral Mutation Section is implementing this knowledge to develop novel therapeutic agents and strategies to control HIV infection. Dr. Pathak’s innovative genome tracking methods proved invaluable in discovering the origin of a newly identified virus, XMRV, and in quelling a potential public health crisis by refuting the controversial claims associating this virus with chronic fatigue syndrome and prostate cancer.
HIV-1 Replication, Host Restriction Factors, Antiviral Drug Resistance, and Development of Novel Therapeutics
Project 1. Develop Novel Therapeutics by Targeting Vif-APOBEC3 Interactions. Inhibition of Deltavif HIV-1 by APOBEC3G (A3G) and APOBEC3F (A3F) requires their expression in the virus producer cells and incorporation into virions. A3G and A3F deaminate cytidines in minus-strand DNA, causing G-to-A hypermutation and inhibiting viral DNA synthesis. HIV-1 Vif (Vif1) overcomes these host defenses by targeting A3G and A3F for proteasomal degradation. The Vif1-A3G and Vif1-A3F interactions provide two potential targets for development of pharmacological agents that interfere with Vif1-mediated degradation of A3G and A3F (Xu et al., PNAS, 2004; Russell et al., J. Virol., 2007; Smith & Pathak, J. Virol. 2010). To identify such small-molecule inhibitors, we have developed cell-based high-throughput assays and we are collaborating with the National Center for Advancing Translational Sciences (NCATS) to identify molecules that specifically inhibit the Vif1-A3G and Vif1-A3F interactions. Vif1 binds to several host proteasomal proteins; we are collaborating with the NCATS to carry out a small-interfering-RNA (siRNA) screen to identify host factors that may be involved in Vif1-mediated degradation of A3G and A3F. Gene therapy for HIV-1 infected individuals has the potential to provide a one-time treatment that will reduce viral load, lessen the use of toxic antiviral drugs, and preserve or improve immune function. Our goal is to test the hypothesis that expression of Vif1-resistant A3G and A3F proteins in HIV-1 target cells will reduce viral loads and control HIV-1 replication. We are developing novel retroviral vectors that can efficiently deliver the Vif1-resistant A3G and A3F to hematopoietic stem cells, and will use a humanized mouse model system to determine the effect of the gene therapy on HIV-1 viral load and preservation of CD4+ T cells. These studies will provide the proof of concept that gene therapy with Vif1-resistant A3G and A3F can provide an effective treatment for HIV-1 infection.
Project 2. Elucidate the Structure and Function of APOBEC3 Proteins. We have shown that A3G and A3F both inhibit viral DNA integration, but through distinctly different mechanisms (Mbisa et al., J. Virol., 2007; Mbisa et al., J. Virol., 2010). We also developed a bimolecular fluorescence complementation assay to visualize A3G and A3F molecular interactions in living cells and observed that A3G and A3F multimerization, A3G-Gag interactions, and A3G virion incorporation require RNA binding (Friew et al., Retrovirology, 2009). We recently compared the antiviral activity of A3G and A3F in primary CD4+ T cells and macrophages, the natural target cells of infection, and found that while both can inhibit HIV-1 replication A3G is a more potent inhibitor of HIV-1 than A3F (Chaipan et al., J. Virol., 2013). We recently showed for the first time that A3G and A3F remain associated with HIV-1 preintegration complexes (PICs) in the nuclei of infected cells (Burdick et al., PNAS, 2013). Using A3F-labeling as a novel tool to visualize PICs, we determined that 1) reverse transcription is not required for nuclear import of PICs, indicating that a viral core uncoating event associated with reverse transcription, and the central DNA flap that forms during reverse transcription, are not required for nuclear import; 2) viral core stability mutations dramatically reduce association of PICs with the nuclear envelope as well as diminish their nuclear import; and 3) most nuclear PICs remain close to the nuclear envelope and are not distributed throughout the nuclei. We are also analyzing HIV-2 Vif (Vif2) interactions with A3G and A3F and find that these structural determinants are different from the Vif1-A3G and Vif1-A3F interaction determinants. Hypermutation by A3G and A3F can potentially contribute to viral genetic variation and evolution. We have observed that replication of a Vif1 mutant defective in blocking A3G exhibits strong purifying selection at multiple steps in viral replication (Russell et al., Retrovirology, 2009). We are analyzing replication of Vif1 mutants defective in blocking A3G or A3F by ultra-deep pyrosequencing to gain a comprehensive view of the impact of APOBEC3 proteins on HIV-1 genetic diversity, selection, and evolution.
Project 3. Explore Mechanisms of Antiviral Drug Resistance, Host Factors, and Retroviral Replication. Most studies of clinical drug resistance to nucleoside and nonnucleoside reverse transcriptase (RT) inhibitors (NRTIs and NNRTIs, respectively) analyze the first 300 amino acids of RT and do not include the C-terminal connection subdomain (CN) or the RNase H domain (RH). We observed that several mutations in the CN and RH reduce RNase H activity, thereby affecting the balance between RNA degradation and nucleotide excision and enhancing NRTI resistance ( Nikolenko et al., PNAS, 2005; Nikolenko et al., PNAS, 2007; Delviks-Frankenberry et al., PNAS, 2008). Our studies have demonstrated that mutations in the CN and the RH can also increase resistance to NNRTIs, and suggest a parallel mechanism by which resistance to both classes of RT inhibitors can be increased (Nikolenko et al., J. Virol., 2010). It has been observed that CN mutations are present in drug-naive patients, and we are exploring the mechanisms by which CN mutations may be selected prior to initiation of antiviral therapy.
While investigating the functional relevance of A3G localization to P bodies, we found that P body-associated protein Mov10 potently inhibits HIV-1 replication by reducing virus production and inhibiting reverse transcription (Burdick et al., J. Virol., 2010). We are elucidating the mechanism by which Mov10 inhibits HIV-1 replication, and found that association of Mov10 and A3G with cytoplasmic mRNA processing bodies is not required for their virion incorporation and antiviral activity (Izumi et al., J. Virol., 2013).
Xenotropic murine leukemia virus-related virus (XMRV), a gammaretrovirus, was reportedly found in prostate cancer (PC) and chronic fatigue syndrome (CFS) patients at high frequencies. However, we found that XMRV replication is severely restricted by human APOBEC3 proteins (Paprotka et al., J. Virol., 2010) and XMRV and spread are severely restricted in human peripheral blood mononuclear cells (PBMCs) (Chaipan et al., J. Virol., 2011), raising doubts about robust XMRV replication in these cells as previously reported. To gain insights into the origin of XMRV, we analyzed PC xenografts that were passaged in nude mice and used to develop a cell line that produces XMRV that is nearly identical to the viruses isolated from patients. The results showed that XMRV is most likely a recombinant between two murine endogenous proviruses that we named PreXMRV-1 and PreXMRV-2 (Paprotka et al., Science, 2011). We concluded that the association between XMRV and human disease is due to contamination of human samples with virus originating from this unique recombination event.
Selected Key Publications
Minimal contribution of APOBEC3-induced G-to-A hypermutation to HIV-1 recombination and genetic variation.12(5): e1005646, 2016. [ Journal Article ]
- Nucleic Acids Res.. 44: 7848-7865, 2016. [ Journal Article ]
- Proc Natl Acad Sci U S A Plus. 110: E4780-9, 2013. [ Journal Article ]
- Science. 333: 97-101, 2011. [ Journal Article ]
HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision.Proc. Natl. Acad. Sci. U.S.A. 105: 10943-10948, 2008. [ Journal Article ]
Dr. Vinay K. Pathak received his B.A. in Biology from the University of California, Los Angeles, in 1979. He obtained his M.S. in Comparative Pathology in 1983 from the University of California, Davis, for characterization of mouse mammary tumor virus proviral integration sites near the int1 and int2 loci in mammary tumors and hyperplastic tissues in Dr. Robert Cardiff's laboratory. He received his Ph.D. for work on characterization of the eukaryotic protein synthesis initiation factors eIF-2α and eIF-2β in Dr. John W.B. Hershey's laboratory at the University of California, Davis, in 1988. He was a postdoctoral fellow under the guidance of Dr. Howard Temin from 1988 to 1991, where he determined the in vivo forward mutation rate of spleen necrosis virus and characterized the nature of mutations that arise during retroviral replication. These studies were the first to report G-to-A hypermutation in a retrovirus, now known to be the result of cytidine deamination by host restriction APOBEC3 proteins. In 1991, Dr. Pathak became an Assistant Professor in the Department of Biochemistry and the Mary Babb Randolph Cancer Center at West Virginia University. He was promoted to Associate Professor with tenure in 1998. He joined the National Cancer Institute in 1999 as Senior Investigator and Head of the Viral Mutation Section in the HIV Dynamics and Replication Program (renamed as the HIV Dynamics and Replication Program in 2015). Dr. Pathak was appointed as Guest Editor for the "HIV Drug Resistance" special issue of Viruses, published in 2010. In 2012, he received the NIH Asian and Pacific Islander American Organization Award for outstanding accomplishments in biomedical research. He served as Co-Chair (2013-2014) and Chair (2015) of the Annual Norman P. Salzman Memorial Symposium in Virology, NIH. In 2017, he served as Co-Organizer of the Cold Spring Harbor Laboratory Retroviruses Meeting. He currently serves as a member of the NCI RNA Biology Initiative.
|Ryan Burdick M.S.||Research Biologist|
|John Chen M.S.||Postbaccalaureate Fellow (CRTA)|
|Krista A. Delviks-Frankenberry, Ph.D.||Staff Scientist|
|Belete A. Desimmie Ph.D.||Postdoctoral Fellow (Visiting)|
|Chenglei Li Ph.D.||Postdoctoral Fellow (Visiting)|
|Mohamed Husen Munshi Ph.D.||Postdoctoral Fellow (Visiting)|
|Michael Nekorchuk Ph.D.||Postdoctoral Fellow (CRTA)|
Young Investigator Awards, Conference on Retroviruses and Opportunistic Infections
Belete Desimmie received a Young Investigator Award to present his research findings at the 2017 Conference on Retroviruses and Opportunistic Infections (CROI). In 2013, Taisuke Izumi also received this highly selective CROI travel scholarship.
Norman P. Salzman Memorial Poster Award in Virology
Belete Desimmie won a 2016 Norman P. Salzman Memorial Poster Award in Virology for his work on APOBEC3 inhibition of HIV-1 replication. This annual NIH-wide award is given to three postdoctoral fellows per year to recognize outstanding research in the field of virology under the mentorship of an NIH, CBER, or Leidos scientist. Postdoctoral fellows from all NIH campuses, including Bethesda and Frederick, can apply for the award. Dr. Desimmie presented his poster at the 18th Annual Norman P. Salzman Virology Symposium in November 2016 and received a cash award for his achievement.
NIH Fellows Awards for Research Excellence
The NIH Fellows Award for Research Excellence (FARE) acknowledges outstanding scientific research performed by intramural postdoctoral fellows. This award is sponsored by the NIH Fellows Committee, Scientific Directors, and Office of Intramural Training and Education and is funded by the Scientific Directors. Awards are based on scientific merit, originality, experimental design, and overall quality/presentation of the abstracts. Sanath Kumar Janaka was awarded a 2017 FARE stipend for travel to attend and present his work at a scientific meeting in the U.S. Members of the Pathak lab who were FARE awardees in previous years include Tobias Paprotka (2012), Narasimhan Jayanth Venkatachari (2012), Wei Bu (2010), Jessica Smith (2010), Rebecca Russell (2009), Krista Delviks-Frankenberry (2008), Yeshitila Friew (2007), Patricia Henry (2007), and Galina Nikolenko (2007).
Intramural AIDS Research Fellowships
The following Postdoctoral Fellows in the Pathak lab received Intramural AIDS Research Fellowship (IARF) awards from the Office of AIDS Research, Office of Intramural Research, and Office of Intramural Research & Training in the National Institutes of Health to support their proposed research projects:
Belete Desimmie: "Identification of Novel Class of HIV Replication Inhibitors Targeting the HIV-1 Vif-A3G Interactions" (2014)
Narasimhan Jayanth Venkatachari: "Identification of Small Molecule Inhibitors of Vif-A3G and Vif-A3F Interactions as Novel Antiviral Agents for the Treatment of HIV-1 Infection" (2010, 2011)
IARF awards include full stipend support to successful candidates who demonstrate outstanding scientific potential through both an imaginative and thoughtful research plan and a well thought out career development plan.
Poster Awards, Spring Research Festival at NCI-Frederick
Taisuke Izumi won a poster award for his presentation at the 2013 NCI-Frederick Spring Research Festival. Members of the Pathak lab who won poster awards at the Spring Research Festival in previous years include Tobias Paprotka (2011), Krista Delviks-Frankenberry (2007), Rebecca Russell (2007), Patricia Henry (2006), Galina Nikolenko (2006), and Hongzhan Xu (2006).
2013 Awards from Frederick County Science & Engineering Fair
In 2013, Catoctin High School senior Maria Hamscher presented the research she has been conducting in the lab of Dr. Vinay K. Pathak at the 32nd Annual Frederick County Science & Engineering Fair in Frederick, Maryland. Maria won the 2nd Place Award in Cellular & Molecular Biology, High School Division and also a Distinguishing Achievement 2nd Place Award, given by the Commissioned Officers Association of the U.S. Public Health Service, for her research entitled "Testing the P2A Cleavage System for Gene Therapy Vectors." Since July 2012, she has been working as a Werner H. Kirsten Student Intern in the Pathak lab under the mentorship of Dr. Krista Delviks-Frankenberry.
NIH Asian and Pacific Islander American Organization Award
Vinay Pathak was the recipient of the 2012 NIH Asian and Pacific Islander American Organization (APAO) Award for outstanding accomplishments in biomedical research. Each year, the APAO honors two outstanding individuals in the NIH Asian and Pacific American community: one for Scientific Achievement, recognizing scientists who have made significant accomplishments in biomedical research; and the second for Leadership Excellence, recognizing non-scientists who exemplify leadership excellence by example, mentorship, and empowerment of Asian and Pacific Americans to promote diversity and support the overall mission of NIH. Dr. Pathak received his Scientific Achievement award at the NIH APAO annual awards ceremony in December 2012.
NIH APAO Award for Scientific Achievement — December 10, 2012
Award from U.S.-Russia Joint Working Group on Biomedical Research Cooperation
In 2012, Vinay Pathak was the recipient of one of the five grants that the U.S.-Russia Joint Working Group on Biomedical Research Cooperation awarded to National Cancer Institute intramural investigators for their highly meritorious research applications. Dr. Pathak is the Principal Investigator on a project focused on characterizing broadly neutralizing antibodies by phage display peptide libraries.
Norman P. Salzman Memorial Award in Virology
Tobias Paprotka won the 2011 Norman P. Salzman Memorial Award in Virology for his work on XMRV. This annual NIH-wide award is given to only one postdoctoral fellow per year to recognize outstanding research in the field of virology under the mentorship of an NIH, Center for Biologics Evaluation and Research, or SAIC scientist. Postdoctoral fellows from all NIH campuses, including Bethesda and Frederick, can apply for the award. Dr. Paprotka presented his research at the Thirteenth Annual Norman P. Salzman Memorial Symposium in Virology on November 10, 2011 and received a plaque and a cash award for his achievement. As Dr. Paprotka's mentor, Vinay Pathak also received a plaque at the Symposium.
Postdoctoral Fellowship, Japan Society for the Promotion of Science
Taisuke Izumi was awarded a Postdoctoral Fellowship from 2011 to 2013 by the Japan Society for the Promotion of Science. The fellowship program sponsored by this society supports meritorious biomedical research projects undertaken in NIH laboratories by Japanese postdoctoral researchers. Fellowships are awarded after a competitive review of research proposals.
Scholarship Award, Keystone Symposia on HIV Pathogenesis
Rebecca Russell was awarded a travel scholarship to present her research findings at the 2008 Keystone Symposia on HIV Pathogenesis.
2006 Travel Fellowship, HIV & Cancer Virology Faculty, Center for Cancer Research
In 2006, Jean L. Mbisa won one of the three available travel fellowships awarded by the HIV & Cancer Virology Faculty, Center for Cancer Research, National Cancer Institute.