Mellors Laboratory

The Mellors Laboratory performs basic and translational research with the goals of making advances in HIV-1 prevention, treatment and cure. Prevention and treatment research programs focus on the molecular mechanisms, epidemiology and clinical significance of HIV-1 resistance to antiretroviral drugs that are used for both treatment and prevention. HIV-1 cure research focuses on characterizing the cellular and anatomic sites of HIV-1 persistence, how integration sites of HIV-1 proviruses in the human genome affect viral and host cell biology, and on innovative therapeutic strategies to deplete the reservoirs of HIV-1 within a host or control HIV-1 replication after antiretroviral therapy is stopped. The laboratory provides a dynamic and productive research environment that consists of research specialists, doctoral students, medical students, junior research faculty, and visiting international scholars. It is supported by the NIH, the Bill and Melinda Gates Foundation, and collaborations with industry.

Dr. Mellors’ other roles related to his laboratory research include principal investigator of the NIH DAIDS-funded Pitt Clinical Trials Unit and Director of the Virology Cores for the NIH-funded AIDS Clinical Trials Group and the Microbicides Trials Network. These roles provide access to important samples from cohort studies and interventional trials for translational research studies.

 

Contributions to Science


Mechanisms and clinical significance of HIV-1 resistance to antiretroviral drugs

Starting in late 1980’s, the Mellors Laboratory sought to understand whether or not HIV-1 could develop resistance to antiretroviral agents that were either in development or clinical use at the time. These efforts led to the discovery of new resistance mutations to nucleoside reverse transcriptase inhibitors (3TC: M184V [ref 1]), pyrophosphate analogs (W88G/S; Q161L; H208Y [ref 2]), and nonnucleoside RT inhibitors (TIBO R82150; L100I). Antagonistic interactions between resistance mutations, such as K65R and thymidine analog mutations [ref 3], were discovered and the biochemical basis of bidirectional antagonism between mechanisms of nucleoside discrimination and excision was shown. The clinical significance of HIV-1 drug resistance was shown in a multi-study analysis that Dr. Mellors led of response to salvage antiretroviral treatment regimens that revealed, for the first time, the predictive value for treatment response  of genotypic and phenotypic sensitivity scores (GSS and PSS), which have since been used universally to assess antiretroviral regimen activity [ref 4]. Current work continues to characterize cross-resistance between antiretrovirals being used for both HIV-1 treatment and prevention including nucleoside reverse transcriptase (RT) inhibitors (tenofovir, 3TC, FTC), non-nucleoside RT inhibitors (efavirenz, rilpivirine and dapivirine) [ref 5-8], and integrase inhibitors (raltegravir, cabotegravir, dolutegravir), especially in low- and middle-income countries [ref 9].

  1. Schinazi RF, Lloyd RM, Nguyen M-H, Cannon D, Ilksoy N, Chu CK, Liotta DC, Mellors JW. Characterization of human immunodeficiency viruses resistant to oxathiolane-cytosine nucleosides. Antimicrob Agents Chemother 1993; 37:875-881. PMCID: PMC187791.
  2. Mellors JW, Bazmi H, Weir J, Arnold E, Schinazi R, Mayers D. Novel mutations in reverse transcriptase of human immunodeficiency virus type-1 reduce susceptibility to foscarnet in laboratory and clinical isolates. Antimicrob Agents Chemother 1995; 39:1087-1092. PMCID: PMC162688.
  3. Bazmi HZ, Hammond JL, Cavalcanti SCG, Chu CK, Schinazi RF, Mellors JW. In vitro selection of mutations in HIV-1 reverse transcriptase that decrease susceptibility to (-) b-D-dioxolane-guanosine and suppress resistance to 3’-azido-3’-deoxythymidine. Antimicrob Agents Chemother 2000; 44:1783-1788. PMCID: PMC89962.
  4. DeGruttola V, Dix L, D’Aquila R, Holder D, Phillips A, Ait-Kahled M, Baxter J, Clevenberg, P, Hammer S, Harrigan R, Katzenstein D, Lanier R, Miller M, Para M, Yerly S, Zolopa A, Murray J, Patick A, Miller V, Castillo S, Pedneault L, Mellors JW. The relation between baseline HIV drug resistance and response to antiretroviral therapy: Re-analysis of retrospective and prospective studies using a standardized data analysis plan. Antiviral Therapy 2000; 5:41-48.
  5. Penrose KJ, Parikh UM, Hamanishi KA, Else L, Back D, Boffito M, Jackson A, Mellors JW. Selection of rilpivirine-resistant HIV-1 in a seroconverter from the SSAT 040 Trial who received the 300-mg dose of long-acting rilpivirine (TMC278LA). J Infect Dis. 2015 Nov 12. pii: jiv528. [Epub ahead of print] PMID: 26563240. PMCID: PMC5278732.
  6. Penrose KJ, Wallis CL, Brumme CJ, Hamanishi KA, Gordon KC, Viana RV, Harrigan PR, Mellors JW, Parikh UM. Frequent cross-resistance to dapivirine in HIV-1 Subtype C-infected individuals after first-Line antiretroviral therapy failure in South Africa. Antimicrob Agents Chemother. 2017 Jan 24;61(2). pii: e01805-16. doi: 10.1128/AAC.01805-16. Print 2017 Feb. PMID: 27895013. PMCID: PMC528732.
  7. Parikh UM, Mellors JW. Should we fear resistance from tenofovir/emtricitabine preexposure prophylaxis? Curr Opin HIV AIDS. 2016 Jan;11(1):49-55. doi: 10.1097. PMID: 26633640.
  8. Penrose KJ, Brumme CJ, Scoulos-Hanson M, Hamanishi K, Gordon K, Riana RV, Wallis CL, Mellors JW, Parikh UM. Frequent cross-resistance to rilpivirine among subtype C HIV-1 from first-line antiretroviral therapy failurs in South Africa. Antivir Chem Chemother. Antivir Chem Chemother. 2018 Jan-Dec;26:2040206618762985. doi: 10.1177/2040206618762985. PMID: 29566538. PMCID: PMC5890541.
  9. Wallis CL, Godfrey C, Fitzgibbon JE, Mellors JW. Key factors influencing the emergence of human immunodeficiency virus drug resistance in low- and middle-income countries. J Infect Dis. 2017 Dec 1;216(suppl 9):S851-S856. PMID 29207000. PMCID: PMC5853971.


Viremia in HIV-1 infection

The Mellors Laboratory led several studies with samples from the multicenter AIDS cohort study (MACS) that established the critical relationship between plasma viremia (HIV-1 RNA) and HIV disease progression to AIDS and death in both acute and chronic HIV-1 infection [refs 1, 2]. This work led to the universal use of plasma HIV-1 RNA and CD4+T-cell counts to estimate prognosis in HIV-1 infection and timing of antiretroviral therapy [ref 3]. The importance of viremia as the key driver of disease pathogenesis was challenged in mid-2000’s but further analyses of data from the MACS cohort refuted this thesis and revealed flaws in the analysis that had led to it [ref 4]. Recent and current work continues on quantifying the persistence of low-level viremia in persons on clinically effective antiretroviral therapy and identifying the cellular and anatomic sources of persistent viremia as a step toward eliminating them [ref 5, 6].

  1. Mellors JW, Kingsley LK, Rinaldo CR, Todd J, Hoo B, Kokka RP, Gupta P. Quantitation of HIV-1 RNA in plasma predicts outcome after seroconversion. Ann Intern Med 1995; 122:573-579.
  2. Mellors JW, Rinaldo CR, Gupta P, White RM, Todd JA, Kingsley LA. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science, 1996; 272:1167-1170.
  3. Mellors JW, Munoz A, Giorgi JV, Margolick JB, Tassoni CJ, Gupta P, Kingsley LA, Todd JA, Schrager LK, Saah AJ, Detels RR, Phair JP, Rinaldo CR. Plasma viral load and CD4+T-lymphocytes as prognostic markers in HIV-1 infection.  Ann Intern Med 1997; 126:946-954.
  4. Mellors JW, Margolick JB, Phair JP, Rinaldo CR, Detels R, Jacobson LP, Muñoz A. Prognostic value of HIV-1 RNA, CD4 cell count, and CD4 cell slope for progression to AIDS and death in untreated HIV-1 infection. JAMA 2007;297(21):2349-50. PMID: 17551128.
  5. Cillo AR, Vagratian D, Bedison M, Anderson E, Kearney MF, Fyne E, Koontz D, Coffin JM, Piatak M, Mellors JW. Improved single copy assays for quantification of persistent HIV-1 viremia in patients on suppressive antiretroviral therapy. Clin Microbiol. 2014 Nov,52(11):3944-51. PMID: 25187636. PMCID: PMC4313209.
  6. Riddler SA, Aga E, Bosch RJ, Bastow B, Bedison M, Vagratian D, Vaida F, Eron JJ, Gandhi RT, Mellors JW; ACTG A5276s Protocol Team. Continued slow decay of the residual plasma viremia level in HIV-1-infected adults receiving long-term antiretroviral therapy. J Infect Dis. 2015 Sep 2. pii: jiv433. PMID: 26333941. PMCID: PMC4721905.


Development of effective antiretroviral therapy

The Mellors Lab contributed to the development and testing of the first antiretroviral combinations that produced sustained suppression of viremia [ref 1, 3] and recovery of CD4+T-cells that launched the current era of highly-effective antiretroviral therapy. Dr. Mellors co-led, with Scott Hammer, MD, a large randomized clinical trial of different multi-drug salvage regimens that underscored the need for new antiretroviral agents to treat drug-resistant HIV. Lastly, Drs. Riddler and Mellors, led a randomized trial of antiretroviral therapy that established the superiority of efavirenz over lopinavir/ritonavir for initial treatment [ref 4)]. More recent work has focused on optimal second- and third-line antiretroviral therapy in low- and middle-income countries [ref 5].

  1. Gulick R, Mellors JW, Havlir D, Eron J, Gonzalez C, McMahon D, Richman D, Valentine F, Jonas L, Deutsch P, Meibohm A, Holder D, Schleif W, Condra J, Emini E, Chodakewitz J. Treatment with a combination of indinavir, zidovudine, and lamivudine in HIV-infected adults with prior antiretroviral use. N Engl J Med 1997; 337:734-739.
  2. Hammer SM, Vaida FL, Bennett KS, Holohan MK, Sheiner L, Eron JJ, Wheat LJ, Mitsuyasu RT, Sepkowitz K, Valentine FT, Jacobson MA, Rogers M, Karol C, Saah A, Lewis RH, Manion DJ, Brosgart C, DeGruttola V, Mellors JW. Dual versus single protease inhibitor therapy following antiviral treatment failure: A randomized trial. JAMA 2002; 288:169-180.
  3. Gulick RM, Meibom A, Havlir D, Eron J, Mosley A, Chodakewitz JA, Issacs R, Gonzalez C, McMahon D, Richman DD, Robertson M, Mellors JW. Six-year follow-up of HIV-1 infected adults in a clinical trial of combination antiretroviral therapy with indinavir, zidovudine, and lamivudine. AIDS 2003: 17:2345-2349.
  4. Riddler SA, Haubrich R, DiRienzo AG, Peeples L, Powderly WG, Klingman KL, Garren KW, George T, Rooney JF, Brizz B, Lalloo UG, Murphy RL, Swindells S, Havlir D, Mellors JW for the ACTG Study A5142 Team.  Class-sparing regimens for initial treatment of HIV-1 infection: ACTG 5142. New Eng J Med 2008 May 15; 358:2095-2106. PMID: 18480202. PMCID: PMC3885902.
  5. La Rosa AM, Harrison LJ, Taiwo B, Wallis CL, Zheng L, Kim P, Kumarasamy N, Hosseinipour MC, Jarocki B, Mellors JW, Collier AC, ACTG A5273 Study Group. Raltegravir in second-line antiretroviral therapy in resource-limited settings (SELECT): a randomised, phase 3, non-inferiority study. Lancet HIV. 2016. Jun;3(6): e247-58. PMID: 27240787. PMCID: PMC4914044.


HIV-1 persistence despite antiretroviral therapy and interventions to deplete HIV-1 reservoirs

In recent years, the Mellors Laboratory has focused on mechanisms of HIV-1 persistence and strategies to achieve a cure of HIV-1 infection, defined as prolonged control of viral replication without antiretroviral therapy. This work identified the stable persistence of low-level viremia in most individuals on long-term suppressive ART and showed that the level of this residual viremia is predicted by the level of viremia before ART [ref 1]. Triphasic decay of HIV-infected cells with a stable plateau after 4 years of ART was shown in longitudinal study of persons on suppressive ART for more than 10 years [ref 2]. A method to assess latency reversal at the single proviral level was developed to reveal that only a small fraction of latent proviruses in resting CD4+T-cells from patients can be activated with current latency reversing agents or with T-cell activation [ref 3]. Recently, we showed that most of the HIV reservoir consists of multiple identical copies of intact (replication-competent) proviruses that are likely expanded through CD4+T-cell proliferation, indicating that the reservoir is dynamic rather than static [ref 4] and is most likely maintained through cellular proliferation rather than ongoing replication [ref 5], although the persistence of HIV-infected cells does not appear to be associated with immune activation or inflammation [ref 6].

  1. Maldarelli F, Palmer S, King MS,  Wiegand A, Polis MA, Mican J, Kovacs JA, Davey RT, Rock-Kress D, Dewar R, Liu S, Metcalf JA, Rehm C, Brun SC, Hanna GJ, Kempf DJ, Coffin JM, Mellors JW. ART suppresses plasma HIV-1 RNA to a stable set point predicted by pretherapy viremia. PLoS Pathog 2007;3(4): e46. PMID: 17411338. PMCID: PMC1847689.
  2. Besson GJ, Lalama CM, Bosch RJ, Gandhi RT, Bedison MA, Aga E, Riddler SA, McMahon DK, Hong F, Mellors JW. HIV-1 DNA decay dynamics in blood during more than a decade of suppressive antiretroviral therapy. Clin Infect Dis. 2014 Jul 29. pii: ciu585. PMID: 25073894. PMCID: PMC4200019.
  3. Cillo AR, Sobolewski MD, Bosch RJ, Fyne E, Piatak M, Coffin JM, Mellors JW. Quantification of HIV-1 Latency Reversal in Resting CD4+ T Cells from patients on suppressive antiretroviral therapy. Proc Natl Acad Sci USA. 2014 May 13; 111(19):7078-83. PMID: 24706775. PMCID: PMC4024870.
  4. Bui JK, Sobolewski MD, Keele BF, Spindler J, Musick A, Wiegand A, Luke BT, Shao W, Hughes SH, Coffin JM, Kearney MF, Mellors JW. Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir. PLoS Pathog. 2017 Mar 22;13(3):e1006283. doi: 10.1371/journal.ppat.1006283. [Epub ahead of print] PMID: 28328934. PMCID: PMC5378418.
  5. Van Zyl GU, Katusiime MG, Wiegand A, McManus WR, Bale MJ, Halvas EK, Luke B, Boltz VF, Spindler J, Laughton B, Engelbrecht S, Coffin JM, Cotton MF, Shao W, Mellors JW, Kearney MF. No evidence of HIV replication in children on antiretroviral therapy. J Clin Invest. 2017 Oct 2; 127(10): 3827-3834. PMID: 28891813. PMCID: PMC5617669.
  6. Gandhi RT, McMahon DK, Bosch RJ, Lalama CM, Cyktor JC, Macatangay BJ, Rinaldo CR, Riddler SA, Hogg E, Godfrey C, Collier AC, Eron JJ, Mellors JW; ACTG A5321 Team. Levels of HIV-1 persistence on antiretroviral therapy are not associated with markers of inflammation or activation. PLoS Pathog. 2017 Apr 20; 13(4): e1006285. doi: 10.1371/journal.ppat.1006285. PMID: 28426825. PMC: PMCID: 5398724.
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