TAG HIV Basic Science, Vaccines, and Cure Project Blog

Free Database of Broadly Neutralizing HIV Antibodies

Following up on the prior post about broadly neutralizing antibodies (bNAbs) against HIV, there is now a free database available (http://bnaber.org) that offers detailed information on all known bNAbs. The genesis and purpose of the database is described in an open access paper in the journal Nucleic Acids Research. Although not a focus of the paper, it's worth noting that the discovery of growing numbers of bNAbs has been facilitated by major investments in the research, particularly by National Institutes of Health funding for the Center for HIV/AIDS Vaccine Immunology and, more recently, two Centers for HIV/AIDS Vaccine Immunology & Immunogen Discovery (at Duke University and the Scripps Institute) and also by the non-profit International AIDS Vaccine Initiative (IAVI) though its Neutralizing Antibody Consortium. 

Nucleic Acids Res. 2013 Nov 7. [Epub ahead of print]

bNAber: database of broadly neutralizing HIV antibodies. (open access)

Eroshkin AM, Leblanc A, Weekes D, Post K, Li Z, Rajput A, Butera ST, Burton DR, Godzik A.

Abstract

The discovery of broadly neutralizing antibodies (bNAbs) has provided an enormous impetus to the HIV vaccine research and to entire immunology. The bNAber database at http://bNAber.org provides open, user-friendly access to detailed data on the rapidly growing list of HIV bNAbs, including neutralization profiles, sequences and three-dimensional structures (when available). It also provides an extensive list of visualization and analysis tools, such as heatmaps to analyse neutralization data as well as structure and sequence viewers to correlate bNAbs properties with structural and sequence features of individual antibodies. The goal of the bNAber database is to enable researchers in this field to easily compare and analyse available information on bNAbs thereby supporting efforts to design an effective vaccine for HIV/AIDS. The bNAber database not only provides easy access to data that currently is scattered in the Supplementary Materials sections of individual papers, but also contributes to the development of general standards of data that have to be presented with the discovery of new bNAbs and a universal mechanism of how such data can be shared.

Exploring the Therapeutic Potential of Neutralizing Antibodies

HIV is notoriously stubborn in its ability to thwart attacks by antibodies. The sugary outer envelope of the virus is so effective in cloaking its vulnerabilities that, for many years, the number of antibodies known to have broad neutralizing activity against HIV could be counted on one hand. But recently, collaborative research efforts aiming to identify and isolate more broadly neutralizing antibodies (bNAbs) have paid extraordinary dividends, increasing the number well into double digits and discovering several bNAbs with significantly greater breadth and potency than ever seen before (each isolated antibody is assigned a name, e.g. VRC01, PGT121, etc.). Although the primary impetus for this work is the development of an effective preventive HIV vaccine, there is also interest in exploring whether infusions of these new bNAbs may have therapeutic potential. A study published last year in the journal Nature reported encouraging signs of efficacy in a humanized mouse model, and this past Wednesday two research teams reported similarly promising results in macaque monkeys, drawing considerable media attention. 

The take-home message from both sets of studies is that infusions of either single or combined bNAbs were capable of suppressing viral replication in macaques. The viruses used in the experiments were lab-created hybrids that include the envelope of HIV combined with SIV in order to facilitate the study of anti-HIV antibodies in this animal model; both viruses are pathogenic and cause simian AIDS in macaques. In the paper published by Dan Barouch and colleagues, several additional observations are made that have contributed to the excitement surrounding the work: 

• A subset of macaques (3 of 18) showed prolonged control of SHIV replication to undetectable levels after a single bNAb infusion, which persisted long after the antibodies declined to undetectable levels. This control was associated with increased functionality of virus-specific CD8 T cell responses and enhanced levels of natural neutralizing antibodies in the animals, suggesting that the bNAb infusions had both direct antiviral effects and also indirectly improved virus-specific immune responses. Notably, however, these three macaques had relatively low viral loads at baseline.
• The bNAb infusions were associated with significant declines in SHIV DNA in blood and tissues, indicating a reduction in the persistent viral reservoir, and offering hope that bNAbs could have a role in HIV cure research.
• The declines in viral load appeared faster than is typically seen with antiretroviral therapy (ART), hinting that the bNAbs were accelerating the clearance of virus-infected cells via antibody-mediated effector mechanisms. These mechanisms involve antibodies binding to viral proteins on infected cells and thereby flagging them for clearance by the immune system.

There are a number of potentially important caveats, however. The second paper, by Masashi Shingai and colleagues, involved macaques with more advanced, symptomatic disease and resistance to the bNAbs appeared to develop more easily in this setting (although there were still benefits in terms of reduced viral loads and improved CD4 T cell counts). The Barouch study also found that bNAbs were unable to fully suppress viral load in two macaques with high viral loads at baseline. More generally, it is not yet known if there might be differences between HIV and the lab-created SHIVs when it comes to their ability to develop resistance to bNAbs. Additionally, chronically infected HIV-positive people may harbor more diverse viruses and therefore be more likely to have baseline resistance to some bNAbs compared to SHIV-infected macaques. Early efforts to explore bNAb infusions as therapies were stymied by the development of resistance, but those clinical trials involved first-generation antibodies far less potent than the new crop.

In terms of whether bNAbs might be able to help target HIV-infected cells for destruction, a commentary by Steve Deeks and Louis Picker that accompanies the papers notes that this effector mechanism depends on expression of the viral envelope protein, and “the extent to which viral envelope protein is exposed on the surface of long-lived infected cells is unknown.” At the IAS conference earlier this year there were two presentations that may address this question to a limited degree: on the upside, Victor Garcia showed that in a humanized mouse model, a strategy targeting infected cells via envelope protein expression significantly reduced cell-associated HIV RNA levels when added to ART. On the downside, Rick Koup reported that it was difficult to identify infected CD4 T cells isolated from HIV-positive individuals using envelope-specific bNAbs, even though the cells appeared to be actively transcribing HIV RNA (Koup’s presentation is covered in a report from the conference by David Margolis for NATAP).

Even if productively infected cells can be targeted by bNAbs via envelope expression, Deeks and Picker point out that latently infected cells would not be affected unless the thorny problem of activating latent HIV can be solved. So while bNAbs may be able to offer advantages over ART in the context of cure research, possibly even inducing prolonged containment of viral load in some cases (in the very optimistic scenario in which the results in macaques with low baseline viral loads are duplicated in humans), it is highly unlikely that bNAbs could be fully curative.

Definitive answers regarding the therapeutic efficacy of the new generation of bNAbs can only be obtained from human trials, and it is good news that, this past August, the first such trial got underway at the National Institutes of Health Clinical Research Center. The trial will recruit HIV-positive individuals both on and off ART and evaluate the effects of escalating doses of the bNAb VRC01.

Lastly, there is an overarching issue regarding monoclonal antibody therapies that deserves mention: they are extremely costly to manufacture and, as a consequence, very expensive. Delivery via infusion is also not particularly practical, even though they are typically given intermittently. In part due to these problems, scientists are exploring novel delivery methods such as the use of adeno-associated virus (AAV) vectors as gene therapies that would create long-lived bNAb-making factories in muscle tissue. Examples are David Baltimore’s vectored immunoprophylaxis (VIP) approach (covered previously on the blog) and a construct developed by Philip Johnson from the Children’s Hospital of Philadelphia in collaboration with the International AIDS Vaccine Initiative (IAVI). In the latter case, a phase I clinical trial in HIV-negative volunteers is now pending according to the clinicaltrials.gov database. Although the AAV-based strategy is currently being pursued for prevention, it is perhaps possible that it could be adapted for therapeutic use if bNAb infusions were found to be successful.

Nature (2013) doi:10.1038/nature12744

Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys

Dan H. Barouch, James B. Whitney, Brian Moldt, Florian Klein, Thiago Y. Oliveira, Jinyan Liu, Kathryn E. Stephenson, Hui-Wen Chang, Karthik Shekhar, Sanjana Gupta, Joseph P. Nkolola, Michael S. Seaman, Kaitlin M. Smith, Erica N. Borducchi, Crystal Cabral, Jeffrey Y. Smith, Stephen Blackmore, Srisowmya Sanisetty, James R. Perry, Matthew Beck, Mark G. Lewis, William Rinaldi, Arup K. Chakraborty, Pascal Poignard, Michel C. Nussenzweig et al.

Abstract

Human immunodeficiency virus type 1 (HIV-1)-specific monoclonal antibodies with extraordinary potency and breadth have recently been described. In humanized mice, combinations of monoclonal antibodies have been shown to suppress viraemia, but the therapeutic potential of these monoclonal antibodies has not yet been evaluated in primates with an intact immune system. Here we show that administration of a cocktail of HIV-1-specific monoclonal antibodies, as well as the single glycan-dependent monoclonal antibody PGT121, resulted in a rapid and precipitous decline of plasma viraemia to undetectable levels in rhesus monkeys chronically infected with the pathogenic simian–human immunodeficiency virus SHIV-SF162P3. A single monoclonal antibody infusion afforded up to a 3.1 log decline of plasma viral RNA in 7 days and also reduced proviral DNA in peripheral blood, gastrointestinal mucosa and lymph nodes without the development of viral resistance. Moreover, after monoclonal antibody administration, host Gag-specific T-lymphocyte responses showed improved functionality. Virus rebounded in most animals after a median of 56 days when serum monoclonal antibody titres had declined to undetectable levels, although, notably, a subset of animals maintained long-term virological control in the absence of further monoclonal antibody infusions. These data demonstrate a profound therapeutic effect of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys as well as an impact on host immune responses. Our findings strongly encourage the investigation of monoclonal antibody therapy for HIV-1 in humans.

Nature (2013) doi:10.1038/nature12746

Antibody-mediated immunotherapy of macaques chronically infected with SHIV suppresses viraemia

Masashi Shingai, Yoshiaki Nishimura, Florian Klein, Hugo Mouquet, Olivia K. Donau, Ronald Plishka, Alicia Buckler-White, Michael Seaman, Michael Piatak, Jeffrey D. Lifson, Dimiter Dimitrov, Michel C. Nussenzweig & Malcolm A. Martin

Neutralizing antibodies can confer immunity to primate lentiviruses by blocking infection in macaque models of AIDS^{1, 2, 3, 4}. However, earlier studies of anti-human immunodeficiency virus type 1 (HIV-1) neutralizing antibodies administered to infected individuals or humanized mice reported poor control of virus replication and the rapid emergence of resistant variants^{5, 6, 7}. A new generation of anti-HIV-1 monoclonal antibodies, possessing extraordinary potency and breadth of neutralizing activity, has recently been isolated from infected individuals⁸. These neutralizing antibodies target different regions of the HIV-1 envelope glycoprotein including the CD4-binding site, glycans located in the V1/V2, V3 and V4 regions, and the membrane proximal external region of gp41 (refs 9, 10, 11, 12, 13, 14). Here we have examined two of the new antibodies, directed to the CD4-binding site and the V3 region (3BNC117 and 10-1074, respectively), for their ability to block infection and suppress viraemia in macaques infected with the R5 tropic simian–human immunodeficiency virus (SHIV)-AD8, which emulates many of the pathogenic and immunogenic properties of HIV-1 during infections of rhesus macaques^{15, 16}. Either antibody alone can potently block virus acquisition. When administered individually to recently infected macaques, the 10-1074 antibody caused a rapid decline in virus load to undetectable levels for 4–7 days, followed by virus rebound during which neutralization-resistant variants became detectable. When administered together, a single treatment rapidly suppressed plasma viraemia for 3–5 weeks in some long-term chronically SHIV-infected animals with low CD4+ T-cell levels. A second cycle of anti-HIV-1 monoclonal antibody therapy, administered to two previously treated animals, successfully controlled virus rebound. These results indicate that immunotherapy or a combination of immunotherapy plus conventional antiretroviral drugs might be useful as a treatment for chronically HIV-1-infected individuals experiencing immune dysfunction.