BACKGROUND HIV-1 viremia that is not suppressed by combination antiretroviral therapy (ART) is generally attributed to incomplete medication adherence and/or drug resistance. We evaluated individuals referred by clinicians for nonsuppressible viremia (plasma HIV-1 RNA above 40 copies/mL) despite reported adherence to ART and the absence of drug resistance to the current ART regimen.METHODS Samples were collected from at least 2 time points from 8 donors who had nonsuppressible viremia for more than 6 months. Single templates of HIV-1 RNA obtained from plasma and viral outgrowth of cultured cells and from proviral DNA were amplified by PCR and sequenced for evidence of clones of cells that produced infectious viruses. Clones were confirmed by host-proviral integration site analysis.RESULTS HIV-1 genomic RNA with identical sequences were identified in plasma samples from all 8 donors. The identical viral RNA sequences did not change over time and did not evolve resistance to the ART regimen. In 4 of the donors, viral RNA sequences obtained from plasma matched those sequences from viral outgrowth cultures, indicating that the viruses were replication competent. Integration sites for infectious proviruses from those 4 donors were mapped to the introns of the MATR3, ZNF268, ZNF721/ABCA11P, and ABCA11P genes. The sizes of the clones were estimated to be from 50 million to 350 million cells.CONCLUSION These findings show that clones of HIV-1–infected cells producing virus can cause failure of ART to suppress viremia. The mechanisms involved in clonal expansion and persistence need to be defined to effectively target viremia and the HIV-1 reservoir.FUNDING National Cancer Institute, NIH; Howard Hughes Medical Research Fellows Program, Howard Hughes Medical Institute; Bill and Melinda Gates Foundation; Office of AIDS Research; American Cancer Society; National Cancer Institute through a Leidos subcontract; National Institute for Allergy and Infectious Diseases, NIH, to the I4C Martin Delaney Collaboratory; University of Rochester Center for AIDS Research and University of Rochester HIV/AIDS Clinical Trials Unit.
Elias K. Halvas, Kevin W. Joseph, Leah D. Brandt, Shuang Guo, Michele D. Sobolewski, Jana L. Jacobs, Camille Tumiotto, John K. Bui, Joshua C. Cyktor, Brandon F. Keele, Gene D. Morse, Michael J. Bale, Wei Shao, Mary F. Kearney, John M. Coffin, Jason W. Rausch, Xiaolin Wu, Stephen H. Hughes, John W. Mellors
After over three decades of research, an effective anti-HIV vaccine remains elusive. The recently halted HVTN702 clinical trial not only further stresses the challenge to develop an effective HIV vaccine, but also emphasizes that unconventional and novel vaccine strategies are urgently needed. Here, we report that a vaccine focusing the immune response on the sequences surrounding the 12 viral protease cleavage sites (PCSs) provided greater than 80% protection to Mauritian cynomolgus macaques (MCMs) against repeated intravaginal SIVmac251 challenges. The PCS-specific T cell responses correlated with vaccine efficacy. The PCS vaccine did not induce immune activation or inflammation known to be associated with increased susceptibility to HIV infection. Machine learning analyses revealed that the immune microenvironment generated by the PCS vaccine was predictive of vaccine efficacy. Our study demonstrates for the first time that a vaccine which targets only viral maturation, but lacks full-length Env and Gag immunogens, can prevent intravaginal infection in a stringent macaque/SIV challenge model. Targeting HIV maturation thus offers a novel approach to developing an effective HIV vaccine.
Hongzhao Li, Robert W. Omange, Binhua Liang, Nikki Toledo, Yan Hai, Lewis R. Liu, Dane Schalk, Jose Crecente-Campo, Tamara G. Dacoba, Andrew B. Lambe, So-Yon Lim, Lin Li, Mohammad Abul Kashem, Yanmin Wan, Jorge F. Correia-Pinto, Michael S. Seaman, Xiao-Qing Liu, Robert F. Balshaw, Qingsheng Li, Nancy Schultz-Darken, Maria Jose Alonso, Francis A. Plummer, James B. Whitney, Ma Luo
The development of broadly neutralizing antibodies (BNAbs) in HIV infection is a result of long-term co-evolutionary interaction between viruses and antibodies. Understanding how this interaction promotes the increase of neutralization breadth during infection will improve the way in which we design AIDS vaccine strategies. In this paper, we used SIV-infected rhesus macaques as a model to study the development of neutralization breadth by infecting rhesus macaques with longitudinal NAb escape variants and evaluating the kinetics of NAb response and viral evolution. We found that the infected macaques developed a stepwise NAb response against escape variants and increased neutralization breadth during the course of infection. Furthermore, the increase of neutralization breadth correlated with the duration of infection but was independent of properties of the inoculum, viral loads or viral diversity during infection. These results imply that the duration of infection was the main factor driving the development of BNabs. These data suggest the importance of novel immunization strategies to induce effective NAb response against HIV infection by mimicking long-term infection.
Fan Wu, Ilnour Ourmanov, Andrea Kirmaier, Sivan Leviyang, Celia LaBranche, Jinghe Huang, Sonya Whitted, Kenta Matsuda, David Montefiori, Vanessa M. Hirsch
The correlation of HIV-specific Antibody-Dependent Cellular Cytotoxicity (ADCC) responses with protection from, and delayed progression of HIV-1 infection provides a rationale to leverage ADCC-mediating antibodies for treatment purposes. We evaluated ADCC mediated by different combinations of two to six neutralizing and non-neutralizing anti-HIV-1-Envelope (Env) monoclonal antibodies (mAbs), using concentrations ≤ 1 µg/mL, to identify combinations effective at targeting latent reservoir HIV-1 viruses (LRVs) from ten individuals. We found that within 2 hours, combinations of three mAbs mediated >30% killing of HIV-infected primary CD4+ T cells in presence of autologous NK cells, with the combination of A32 (C1C2), DH511.2K3 (MPER), and PGT121 (V3) mAbs being the most effective. Increasing the incubation of target and effector cells in presence of mAb combinations from 2 to 24 hours resulted in increased specific killing of infected cells, even with neutralization-resistant viruses. The same combination eliminated reactivated HIV-1 latently-infected cells in an ex vivo qualitative viral outgrowth (QVOA) assay. Therefore, administration of a combination of three mAbs should be considered when planning in vivo studies seeking to eliminate persistently HIV-1 infected cells.
Marina Tuyishime, Carolina Garrido, Shalini Jha, Matthew Moeser, Dieter Mielke, Celia LaBranche, David Montefiori, Barton F. Haynes, Sarah B. Joseph, David M. Margolis, Guido Ferrari
Despite effective antiretroviral therapy, HIV-1-nfected cells continue to produce viral antigens and induce chronic immune exhaustion. We propose to identify HIV-1-suppressing agents which can inhibit HIV-1 reactivation and reduce HIV-1-induced immune activation. Using a novel dual reporter system and a high-throughput drug screen, we identified FDA-approved drugs which can suppress HIV-1 reactivation in both cell line models and CD4+ T cells from virally suppressed, HIV-1-infected individuals. We identified 11 cellular pathways required for HIV-1 reactivation as druggable targets. Using differential expression analysis, gene set enrichment analysis and exon-intron landscape analysis, we examined the impact of drug treatment on the cellular environment at a genome-wide level. We identified a new function of a JAK inhibitor filgotinib which suppresses HIV-1 splicing. First, filgotinib preferentially suppresses spliced HIV-1 RNA transcription. Second, filgotinib suppresses HIV-1-driven aberrant cancer-related gene expression at the integration site. Third, we found that filgotinib suppresses HIV-1 transcription by inhibiting T cell activation and by modulating RNA splicing. Finally, we found that filgotinib treatment reduces the proliferation of HIV-1-infected cells. Overall, the combination of a drug screen and transcriptome analysis provides systemic understanding of cellular targets required for HIV-1 reactivation and drug candidates that may reduce HIV-1-related immune activation.
Yang-Hui Jimmy Yeh, Katharine M. Jenike, Rachela M. Calvi, Jennifer Chiarella, Rebecca Hoh, Steven G. Deeks, Ya-Chi Ho
While the advent of combination antiretroviral therapy (ART) has significantly improved survival, tuberculosis (TB) remains the leading cause of death in the HIV-infected population. We employed Mtb/Simian Immunodeficiency Virus (SIV) co-infected macaques to model Mtb/HIV co-infection and study the impact of ART on TB reactivation due to HIV-infection. While ART significantly reduced viral loads and increased CD4+ T cell counts in whole blood and BAL samples, it did not reduce the relative risk of SIV- induced TB reactivation in ART treated macaques in the early phase of treatment. CD4+ T cells were poorly restored specifically in the lung interstitium, despite their significant restoration in the alveolar compartment of the lung as well as in the periphery. IDO1 induction on myeloid cells in the iBALT likely contributed to dysregulated T cell homing and impaired lung immunity. Thus, while ART is indispensable in controlling viral replication, CD4+ T cells restoration and preventing opportunistic infection, it appears inadequate in reversing clinical signs of TB reactivation during the relatively short duration of ART and follow-up during this study. This warrants modeling concurrent treatment of TB and HIV to potentially reduce the risk of reactivation of TB due to HIV. The current and future studies like this have the potential to inform treatment strategies in patients with Mtb/HIV co-infection.
Shashank R. Ganatra, Allison N. Bucsan, Xavier Alvarez, Shyamesh Kumar, Ayan Chatterjee, Melanie Quezada, Abigail I. Fish, Dhiraj K. Singh, Bindu Singh, Riti Sharan, Tae-Hyung Lee, Uma Shanmugasundaram, Vijayakumar Velu, Shabaana A. Khader, Smriti Mehra, Jyothi Rengarajan, Deepak Kaushal
Proliferation of CD4+ T cells harboring HIV-1 proviruses is a major contributor to viral persistence in people on antiretroviral therapy (ART). To determine whether differential rates of clonal proliferation or HIV-1-specific CTL pressure shape the provirus landscape, we performed the intact proviral DNA assay (IPDA) and obtained 661 near-full length provirus sequences from eight individuals with suppressed viral loads on ART at time points seven years apart. We observed slow decay of intact proviruses but no changes in the proportions of various types of defective proviruses. The proportion of intact proviruses in expanded clones was similar to that of defective proviruses in clones. Intact proviruses observed in clones did not have more escaped CTL epitopes than intact proviruses observed as singlets. Concordantly, total proviruses at later timepoints or observed in clones were not enriched in escaped or unrecognized epitopes. Three individuals with natural control of HIV-1 infection (controllers) on ART, included because controllers have strong HIV-1-specific CTL responses, had a smaller proportion of intact proviruses but a similar distribution of defective provirus types and escaped or unrecognized epitopes as the other individuals. This work suggests that CTL selection does not significantly check clonal proliferation of infected cells or greatly alter the provirus landscape in people on ART.
Annukka A. R. Antar, Katharine M. Jenike, Sunyoung Jang, Danielle N. Rigau, Daniel B. Reeves, Rebecca Hoh, Melissa R. Krone, Jeanne C. Keruly, Richard D. Moore, Joshua T. Schiffer, Bareng A.S. Nonyane, Frederick M. Hecht, Steven G. Deeks, Janet D. Siliciano, Ya-Chi Ho, Robert F. Siliciano
Infusion of the broadly neutralizing antibody VRC01 has been evaluated in HIV-1 chronically infected individuals. Here we studied how VRC01 infusions impacted viral rebound after cessation of antiretroviral therapy (ART) in 18 acutely-treated and durably-suppressed individuals. Viral rebound occurred in all individuals, yet VRC01 infusions modestly delayed rebound and participants who showed a faster decay of VRC01 in serum rebounded more rapidly (Rho=0.60, p=0.03). Participants with strains most sensitive to VRC01 or with VRC01 epitope motifs similar to known VRC01-susceptible strains rebounded later (Rho=-0.70, p<0.03). Upon rebound, HIV-1 sequences were indistinguishable from those sampled at diagnosis. Across the cohort, participant derived Env showed different sensitivity to VRC01 neutralization (including two resistant viruses), yet neutralization sensitivity was similar at diagnosis and post-rebound, indicating the lack of selection for VRC01-resistance during treatment interruption.Our results showed that viremia rebounded despite the absence of HIV-1 adaptation to VRC01 and an average VRC01 trough of 221µg/mL. While VRC01 levels were insufficient to prevent a resurgent infection, knowledge that they did not mediate Env mutations in acute-like viruses is relevant for antibody-based strategies in acute infection.
Evan M. Cale, Hongjun Bai, Meera Bose, Michael A. Messina, Donn Colby, Eric Sanders-Buell, Bethany L. Dearlove, Yifan Li, Emily Engeman, Daniel Silas, Anne Marie O’Sullivan, Brendan Mann, Suteeraporn Pinyakorn, Jintana Intasan, Khunthalee Benjapornpong, Carlo Sacdalan, Eugene Kroon, Nittaya Phanuphak, Robert Gramzinski, Sandhya Vasan, Merlin L. Robb, Nelson L. Michael, Rebecca M. Lynch, Robert Bailer, Amélie Pagliuzza, Nicolas Chomont, Amarendra Pegu, Nicole A. Doria-Rose, Lydie Trautmann, Trevor A. Crowell, John Mascola, Jintanat Ananworanich, Sodsai Tovanabutra, Morgane Rolland
The precise mechanism leading to profound immunodeficiency of HIV-infected patients is still only partially understood. Here, we show that more than 80% of CD4 T cells from HIV-infected patients have morphological abnormalities. Their membranes exhibited numerous large abnormal membrane microdomains (aMMDs), which trap and inactivate physiological receptors, such as that for IL-7. In patient plasma, we identified phospholipase A2 group IB (PLA2G1B) as the key molecule responsible for the formation of aMMDs. At physiological concentrations, PLA2G1B synergized with the HIV gp41 envelope protein, which appears to be a driver that targets PLA2G1B to the CD4 T-cell surface. The PLA2G1B/gp41 pair induced CD4 T cell unresponsiveness (anergy). At high concentrations in vitro, PLA2G1B acted alone, independently of gp41, and inhibited the IL-2, IL-4, and IL-7 responses, as well as TCR-mediated activation and proliferation, of CD4 T cells. PLA2G1B also decreased CD4 T-cell survival in vitro, likely playing a role in CD4 lymphopenia in conjunction with its induced IL-7 receptor defects. The effects on CD4 T-cell anergy could be blocked by a PLA2G1B-specific neutralizing mAb in vitro and in vivo. The PLA2G1B/gp41 pair constitutes a new mechanism of immune dysfunction and a compelling target for boosting immune responses in HIV-infected patients.
Julien Pothlichet, Thierry Rose, Florence Bugault, Louise Jeammet, Annalisa Meola, Ahmed Haouz, Frederick Saul, David Geny, José Alcami, Ezequiel Ruiz-Mateos Carmona, Luc Teyton, Gérard Lambeau, Jacques Thèze
Curing HIV infection will require the elimination of a reservoir of infected CD4+ T-cells that persists despite HIV-specific cytotoxic T-cell (CTL) responses. While viral latency is a critical factor in this persistence, recent evidence also suggests a role for intrinsic resistance of reservoir-harboring cells to CTL killing. This resistance may have contributed to negative outcomes of clinical trials, where pharmacologic latency reversal has thus far failed to drive reductions in HIV reservoirs. Through transcriptional profiling, we herein identified over-expression of the pro-survival factor BCL-2 as a distinguishing feature of CD4+ T-cells that survived CTL killing. We show that the inducible HIV reservoir was disproportionately present in BCL-2hi subsets, in ex vivo CD4+ T-cells. Treatment with the BCL-2 antagonist ‘ABT-199’ alone was not sufficient to drive reductions in ex vivo viral reservoirs, when tested either alone or with a latency reversing agent (LRA). However, the triple combination of strong LRAs, HIV-specific T-cells, and a BCL-2 antagonist uniquely enabled the depletion of ex vivo viral reservoirs. Our results provide rationale for novel therapeutic approaches targeting HIV cure and, more generally, suggest consideration of BCL-2 antagonism as a means of enhancing CTL immunotherapy in other settings, such as cancer.
Yanqin Ren, Szu-Han Huang, Shabnum Patel, Winiffer D. Conce Alberto, Dean Magat, Dughan J. Ahimovic, Amanda B. Macedo, Ryan Durga, Dora Chan, Elizabeth Zale, Talia M. Mota, Ronald Truong, Thomas Rohwetter, Chase D. McCann, Colin M. Kovacs, Erika Benko, Avery Wimpelberg, Christopher M. Cannon, W. David Hardy, Alberto Bosque, Catherine M. Bollard, R. Brad Jones