Stephen H. Hughes, Ph.D.

HIV Dynamics and Replication Program
HIV virion image
HIV Dynamics and Replication Program
HIV DRP staff photo September 2019
HIV Dynamics and Replication Program
Melissa Fernandez work-in-progress seminar August 2018
HIV Dynamics and Replication Program
DRP Conference, October 13, 2021
HIV Dynamics and Replication Program
HIV DRP Think Tank Meeting 2017
HIV Dynamics and Replication Program
Sean Patro's poster presentation at CROI 2019
HIV Dynamics and Replication Program
John Coffin and Stephen Hughes participating in This Week in Virology podcast at 2018 Cold Spring Harbor Retroviruses Meeting
HIV Dynamics and Replication Program
Students and postbac fellows in the HIV Dynamics and Replication Program July 2019

Stephen H. Hughes, Ph.D.

Stephen H. Hughes, Ph.D.
Senior Investigator
Head, Vector Design and Replication Section

Dr. Hughes is internationally renowned for his work on the roles of reverse transcriptase (RT) and integrase (IN) in HIV replication.  He is interested in how HIV becomes resistant to RT and IN inhibitors, and in developing drugs that are more effective against the known resistance mutations.  His recent studies focus on HIV integration in individuals.  He serves as Chief of the Retroviral Replication Laboratory and Chief of the Host-Virus Interaction Branch, and from 2006 to 2015 he was Director of the HIV Drug Resistance Program (renamed HIV Dynamics and Replication Program in 2015).

Areas of Expertise

1) HIV replication, 2) retroviruses, 3) antivirals, 4) reverse transcription, 5) integration

HIV-1 Reverse Transcriptase and Integrase

We have a long-standing interest in HIV-1 reverse transcriptase (RT) and, more recently, have begun work on another essential viral enzyme, integrase (IN).  Although much of our work is focused on understanding the mechanisms that underlie drug resistance, and using that information to develop more effective anti-HIV drugs, we are, in both the RT and IN projects, doing experiments that are intended to better understand the roles that these enzymes play in viral replication.  We are also using redirected HIV integration as a tool to investigate chromatin structure and function and a tool to investigate the nature and origin of the HIV reservoir in patients on antiretroviral therapy.

Background.  HIV-1 is the causative agent of AIDS.  The three viral enzymes — RT, IN, and protease (PR) — have essential roles in the replication of HIV-1 and are the targets for all of the most potent anti-HIV drugs.  Although considerable progress has been made in treating HIV-infected patients with three- and four-drug regimens, there is an immediate need for the development of effective ways to prevent new infections.  A potent preventive vaccine would be ideal; however, despite a huge effort, the goal of developing an effective vaccine remains elusive. In the absence of an effective vaccine, reducing the transmission of HIV-1 must rely on barrier methods and/or drug treatments.  There are two ways that anti-HIV drugs can be used to reduce viral transmission: (1) effective therapy in infected patients can reduce the viral load, making it less likely that an infected individual will transmit the virus to a partner; and (2) treating the uninfected partner with an anti-HIV drug can block transmission.  Because most new infections are caused by a single virus, blocking transmission is an attractive option and there is now good evidence that giving an anti-HIV drug to the uninfected partner can significantly reduce viral transmission if the uninfected partner is compliant.  Because of the problem of drug resistance, it would be better to use drugs with nonoverlapping resistance profiles for treatment and prophylaxis.  Treatment would have to be long term and, for this reason, drug toxicity is an important consideration, which argues against the use of nucleoside RT inhibitors (NRTIs).  It would also be better to block infection before the viral DNA is integrated, which argues against the use of PR inhibitors.  Therefore, the two remaining options among the major classes of anti-HIV drugs are nonnucleoside RT inhibitors (NNRTIs) and IN strand-transfer inhibitors (INSTIs).  We are using a combined approach that involves structural analysis, biochemistry, virology, modeling, toxicity testing, and chemistry to design, synthesize, and evaluate new NNRTIs and INSTIs.  We have made good progress in developing new compounds that are effective against the wild-type (WT) and common drug-resistant viruses and that have good therapeutic indexes in tests done in cultured cells.

HIV-1 RT.  There are two clinically important classes of inhibitors of HIV-1 RT: NRTIs and NNRTIs.  In the past, a major focus of our work has been on the mechanism(s) of RT inhibitor resistance.  There is, at this point, a reasonably good understanding of the mechanism(s) of NNRTI resistance, and considerable progress has been made in understanding NRTI resistance, although some important issues remain.  We are continuing to investigate the mechanisms of resistance to nucleoside analogs (NRTIs), and we are also interested in elucidating the mechanism of action of compounds that do not cause an immediate or complete block to DNA synthesis.  However, in terms of developing new anti-HIV compounds, we have shifted our focus to NNRTIs.  Our chemistry collaborators, Drs. Joel Schneider, Gary Pauly, and Craig Thomas, have developed several promising compounds that are able to inhibit, in a one-round replication assay, WT and several common NNRTI-resistant viruses with IC50s below 5 nM.  In cultured cells, these compounds have CC50s that are more than 4 logs higher than their IC50s.  Additional compounds are being designed, synthesized, and tested. Recently, our collaborator, Dr. Zandrea Ambrose, selected a novel resistance mutation with one of our new NNRTIs.  This mutation has some interesting properties (for example, it appears to make the RT of some, but not all, strains of RT temperature sensitive), and we are attempting to understand the mechanisms that underlie the effects of the new mutation.

Almost all of the work that has been done on the mechanisms that underlie drug resistance in HIV-1 RT has been done with RTs from subgroup B viruses.  Although subgroup B is the most common strain in the United States, it is not the major subgroup worldwide.  We are in the process of asking whether the mutations that cause drug resistance in subgroup B RT also have the same effects on drug resistance/susceptability in subgroup C RT.  We are planning to do similar types of experiments comparing the effects of mutation in IN in subgroups B and C.

HIV-1 IN.  Like RT, HIV-1 IN is an important drug target; however, as is the case for all anti-HIV drugs, treatment with INSTIs leads to resistance.  We are making good progress on two fronts: understanding how mutations in IN confer resistance to the currently available compounds, and developing new INSTIs that are effective against the common drug-resistance mutations.  Dr. Terrence Burke is synthesizing new INSTIs and we are testing how these new compounds affect viral replication and measuring their toxicity in cultured cells.  Dr. Peter Cherepanov solved the structures of prototype foamy virus (FV) IN in complex with some of the more promising compounds developed by Dr. Burke.  The active site of FV IN is similar, but not identical, to the active site of HIV-1 IN, and we used Dr. Cherepanov's data to develop models of HIV-1 IN (both WT and mutant).  These models have helped us understand how resistance arises and have been useful in the design of more effective compounds. 

We have recently expanded our collaborative efforts to include the laboratories of Drs. Robert Craigie and Dmitry Lyumkis.  Dr. Craigie’s laboratory makes large amounts of purified recombinant HIV-1 IN (both WT and mutant).  Dr. Lyumkis’s laboratory uses the purified IN to obtain, by cryo-electron microscopy, high-resolution structures of HIV-1 IN in complexes with the ends of the viral DNA and INSTIs.  These structures are at a sufficiently high resolution to show ordered waters, which will be used in drug design and drug development, both by us and by others.  Dr. Burke has recently synthesized several novel compounds that have IC50s in the low nanomolar range in a one-round replication assay.  The best compounds effectively inhibit both WT IN and most of the common drug-resistant variants.  Based on tests done in cultured cells, these compounds have excellent therapeutic indexes (the CC50s are more than 3 logs higher than the IC50s).  With help from the NCI, some of the most promising of the new compounds are being tested for uptake, stability, and toxicity in animals.

We are working with Drs. Xiaolin Wu, Frank Maldarelli, John Coffin, John Mellors, and Mary Kearney to determine the distribution of integration sites in samples obtained from HIV-infected donors.  We previously showed that there is extensive clonal expansion of HIV-infected cells in patients, and that, in some cases, integration of HIV DNA in specific oncogenes (MKL2 and BACH2) can contribute to this clonal expansion.  However, there was a question of whether any of the clonally expanded cells carried an infectious provirus.  We showed not only that there are highly expanded clones on cells that carry infectious proviruses, but also that cells of these clones can release detectable amounts of virus into the blood.  We are analyzing additional infected clones to ask whether clones of cells that carry replication-competent proviruses and clones that carry defective viruses differ in any important way. 

We recently showed that clones of infected cells arise in the first few weeks after a person is infected with HIV.  Some of the clones that arise early can persist for years.  Because there are some experiments that cannot be performed with samples obtained from human donors, we have collaborated with Dr. Jeffrey Lifson to develop a system to study to behavior of simian immunodeficiency virus (SIV)-infected cells in macaques.  In the first set of experiments, we showed that the overall distribution of SIV proviruses/integration sites in macaques is very similar to the overall distribution of HIV proviruses/integration sites in human donors.  We also showed that there is extensive clonal expansion of SIV-infected cells in macaques, and that the infected cells behave in ways that are quite similar to the behavior of HIV-infected cells in humans.  We are now doing experiments to investigate the factors that drive the clonal expansion of HIV-infected cells in humans, and we are asking, in samples obtained from donors on successful antiretroviral therapy, whether the stability of the clones of HIV-infected CD4+ cells is the same as or different from that of clones of uninfected CD4+T cells.

NIH Scientific Focus Areas:
Microbiology and Infectious Diseases, Molecular Biology and Biochemistry, Structural Biology, Virology
  1. Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, Spindler J, Ferris AL, Mellors JW, Kearney MF, Coffin JM, Hughes SH
    Science. 345: 179-183, 2014. [ Journal Article ]
  2. Ferris AL, Wu X, Hughes CM, Stewart C, Smith SJ, Milne TA, Wang GG, Shun MC, Allis CD, Engelman A, Hughes SH
    Proc Natl Acad Sci U S A. 107: 3135-3140, 2010. [ Journal Article ]
  3. Boyer PL, Sarafianos SG, Arnold E, Hughes SH
    J Virol. 75: 4832-4842, 2001.
  4. Federspiel MJ, Bates P, Young JA, Varmus HE, Hughes SH
    Proc Natl Acad Sci U S A. 91: 11241-11245, 1994. [ Journal Article ]
  5. Jacobo-Molina A, Ding J, Nanni RG, Clark AD Jr, Lu X, Tantillo C, Williams RL, Kamer G, Ferris AL, Clark P, Hizi A, Hughes SH, Arnold E
    Proc Natl Acad Sci U S A. 90: 6320-6324, 1993.

Dr. Stephen H. Hughes received his Ph.D. from Harvard University under the direction of Dr. Mario Capecchi and did postdoctoral research under the direction of Drs. J. Michael Bishop and Harold Varmus at the University of California, San Francisco.  From 1979 until 1984, Dr. Hughes was a Senior Staff Investigator at Cold Spring Harbor Laboratory (CSHL).  In 1984 he established the Gene Expression in Eukaryotes Section in the ABL-Basic Research Program at NCI-Frederick.  He became Deputy Director of the ABL-Basic Research Program in 1988 and Director of the Molecular Basis of Carcinogenesis Laboratory in 1995.  In 1999 Dr. Hughes joined the HIV Drug Resistance Program (HIV DRP, renamed as the HIV Dynamics and Replication Program in 2015) in the National Cancer Institute as Chief of the Retroviral Replication Laboratory.  In 2005 he was appointed Acting Director of the HIV DRP and Acting Chief of the Host-Virus Interaction Branch.  He was Director of the HIV DRP from 2006 to 2015. Dr. Hughes is a Co-Organizer of the Annual HIV DRP Conference and the David Derse Memorial Lecture and Award and has served as a Co-Organizer of the CSHL Retroviruses and Viral Vectors Meetings, the Annual Meeting on Oncogenes, and the Keystone Symposium on Pathogenesis and Control of Emerging Infections and Drug Resistant Organisms.  He was named one of the most frequently cited AIDS researchers by Science Watch in 1996.  In 2017 Dr. Hughes was a keynote speaker at the CSHL Retroviruses Meeting and received the 2017 Distinguished Research Career Award from The Ohio State University Center for Retrovirus Research in recognition of his substantial body of work on retroviruses. 

Name Position
Paul L. Boyer Ph.D. Special Volunteer
Dimiter Demirov Ph.D. Research Associate I (Contr)
Andrea L. Ferris M.S. Research Biologist
Shuang (Amber) Guo Ph.D. Scientist I (Contr)
Steven J. Smith Ph.D. Research Biologist
Daria W. Wells M.S. Bioinformatics Analyst I (Contr)
Michael Abram, Ph.D. Visiting Fellow 2005-2010

Current or Last Known Position:
Research Scientist II, Gilead Sciences, Inc., Foster City, CA

Aamir Akram, M.D. Postbaccalaureate Fellow (CRTA) 2013-2015

Current or Last Known Position:
Physician, Frederick, MD

Eugene Barsov, Ph.D. Research Fellow 1999-2001

Current or Last Known Position:
Scientist, Leidos Biomedical Research, Inc., Frederick, MD

Kevin Chang, Ph.D. Postdoctoral Fellow 2001-2007

Current or Last Known Position:
Senior Licensing and Patenting Manager, NIH Office of Technology Transfer, Rockville, MD

Carolyn Crisp, B.S. Postbaccalaureate Fellow (CRTA) 2012-2013

Current or Last Known Position:
Columbia University Mailman School of Public Health, New York, NY

Caroline Davis, Ph.D. Postdoctoral Fellow 2007-2012

Current or Last Known Position:
Complaint Investigation Scientist, Roche Nimblegen, Madison, WI

Mark Driscoll, Ph.D. Research Fellow 1999-2000

Current or Last Known Position:
Co-Founder and Chief Scientific Officer, Shoreline Biome, Farmington, CT

Hong-Qiang Gao, Ph.D. Research Fellow 1999-2000

Current or Last Known Position:

Marie-Pierre Golinelli, Ph.D. Staff Scientist 1999-2001

Current or Last Known Position:
Research Associate, CNRS, Gif-sur-Yvette, France

Gunnar Gunnarsson, Ph.D. Postdoctoral Fellow 2005-2007

Current or Last Known Position:
Specialist, Lyfjastofnun – Icelandic Medicines Control Agency, Seltjarnarnes, Iceland

Barry Johnson, Ph.D. Postdoctoral Fellow (CRTA) 2007-2013

Current or Last Known Position:
Medical Writer, National Cancer Institute, Bethesda, MD

Fatima Jones, Ph.D. Postdoctoral Fellow 2003-2004

Current or Last Known Position:
Senior Scientist, NIH AIDS Research & Reference Reagent Program, Rockville, MD

John Julias, Ph.D. Research Fellow 1999-2006

Current or Last Known Position:
Science & Technology Program Manager, U.S. Department of Homeland Security, Washington, DC

Stanislaw Kaczmarczyk, Ph.D. Research Fellow 2001-2008

Current or Last Known Position:
Scientist, Leidos Biomedical Research, Inc., Frederick, MD

Mary Jane McWilliams, B.A. Research Biologist 1999-2015

Current or Last Known Position:

Jangsuk Oh, Ph.D. Research Fellow 2000-2007

Current or Last Known Position:
Biologist, National Heart, Lung and Blood Institute, Bethesda, MD

Elena Peletskaya, Ph.D. Research Fellow, Guest Scientist 1999-2010

Current or Last Known Position:
Director, Molecular Analytics, Juno Therapeutics, Seattle, WA

Valerian Pinto, Ph.D. Research Fellow 1999-2001

Current or Last Known Position:
Walter Reed Army Institute of Research, Silver Spring, MD

Carolyn Rinke, Ph.D. Predoctoral Fellow 2002

Current or Last Known Position:
Postdoctoral Fellow, Fred Hutchinson Cancer Center, Seattle, W

Amber Steele, Ph.D. Postdoctoral Fellow 2002-2003

Current or Last Known Position:
Patent Examiner, U.S. Patent and Trademark Office, Alexandria, VA

B. Christie Vu, Ph.D. Postdoctoral Fellow 2004-2010

Current or Last Known Position:
Science Officer, U.S. Army Medical Research and Materiel Command, Frederick, MD

Janani Varadarajan, Ph.D. Postdoctoral Fellow (Visiting) 2007-2013

Current or Last Known Position:
Project Manager, Office of Biomedical Research Education & Training, Vanderbilt University, Nashville, TN

Rafal Wierzchoslawski, Ph.D. Research Fellow 2005-2008
Edward Chia-Kuei Wu, Ph.D. Research Fellow 2000-2007

Current or Last Known Position:
Program Project Manager, PATH Malaria Vaccine Initiative, Washington, DC