Germline-like predecessors of broadly neutralizing antibodies lack measurable binding to HIV-1 envelope glycoproteins: Implications for evasion of immune responses and design of vaccine immunogens

Several human monoclonal antibodies (hmAbs) including b12, 2G12, and 2F5 exhibit relatively potent and broad HIV-1-neutralizing activity. However, their elicitation in vivo by vaccine immunogens based on the HIV-1 envelope glycoprotein (Env) has not been successful. We have hypothesized that HIV-1 has evolved a strategy to reduce or eliminate the immunogenicity of the highly conserved epitopes of such antibodies by using “holes” (absence or very weak binding to these epitopes of germline antibodies that is not sufficient to initiate and/or maintain an efficient immune response) in the human germline B cell receptor (BCR) repertoire. To begin to test this hypothesis we have designed germline-like antibodies corresponding most closely to b12, 2G12, and 2F5 as well as to X5, m44, and m46 which are cross-reactive but with relatively modest neutralizing activity as natively occurring antibodies due to size and/or other effects. The germline-like X5, m44, and m46 bound with relatively high affinity to all tested Envs. In contrast, germline-like b12, 2G12, and 2F5 lacked measurable binding to Envs in an ELISA assay although the corresponding mature antibodies did. These results provide initial evidence that Env structures containing conserved vulnerable epitopes may not initiate humoral responses by binding to germline antibodies. Even if such responses are initiated by very weak binding undetectable in our assay it is likely that they will be outcompeted by responses to structures containing the epitopes of X5, m44, m46, and other antibodies that bind germline BCRs with much higher affinity/avidity. This hypothesis, if further supported by data, could contribute to our understanding of how HIV-1 evades immune responses and offer new concepts for design of effective vaccine immunogens.     

基于gp41近膜端外部区域中和表位天然构象的人类免疫缺陷病毒1型疫苗的设计

疫苗一直被视为终结人类免疫缺陷病毒1型和2型(human immunodeficiency virus type 1/2,HIV-1/2)最有力的武器.位于HIV-1 gp41胞外域C末端的近膜端外部区域(membrane-proximal external region,MPER)是一个重要的抗原位点,但糖蛋白41(...     

The development of HIV vaccines targeting gp41 membrane-proximal external region (MPER): challenges and prospects

A human immunodeficiency virus type-1 (HIV-1) vaccine which is able to effectively prevent infection would be the most powerful method of extinguishing pandemic of the acquired immunodeficiency syndrome (AIDS). Yet, achieving such vaccine remains great challenges. The membrane-proximal external region (MPER) is a highly conserved region of the envelope glycoprotein (Env) gp41 subunit near the viral envelope surface, and it plays a key role in membrane fusion. It is also the target of some reported broadly neutralizing antibodies (bNAbs). Thus, MPER is deemed to be one of the most attractive vaccine targets. However, no one can induce these bNAbs by immunization with immunogens containing the MPER sequence(s). The few attempts at developing a vaccine have only resulted in the induction of neutralizing antibodies with quite low potency and limited breadth. Thus far, vaccine failure can be attributed to various characteristics of MPER, such as those involving structure and immunology; therefore, we will focus on these and review the recent progress in the field from the following perspectives: (1) MPER structure and its role in membrane fusion, (2) the epitopes and neutralization mechanisms of MPER-specific bNAbs, as well as the limitations in eliciting neutralizing antibodies, and (3) different strategies for MPER vaccine design and current harvests.     

HIV-1中和抗体和基于抗体的疫苗设计

研制一种安全有效并能广泛使用的HIV疫苗对于预防和控制HIV的流行具有重要的意义。尽管人类在HIV-1病原学和免疫学方面的认识不断取得新的进步,对于HIV-1而言,普遍认为诱导保护性中和抗体的科学障碍很难逾越。在抗击HIV-1的感染中传统的疫苗策略不能提供保护。然而,近来的研究揭示在小部分HIV-1感染病人的血清中存在的某些抗体能够中和大多数的HIV-1毒株,对这些血清抗体的深入分析有助于人们揭示抗体识别的病毒表位,这些研究表明自然产生的能够中和HIV-1的中和抗体的发现可能引导未来疫苗设计的思路。高分辨率的结构信息将揭示Env 和中和抗体(Nab)结合区原子水平的结构,这些信息能够帮助设计更好的免疫原。     

Progress in the rational design of an AIDS vaccine

Human immunodeficiency virus-1 (HIV-1) has a high degree of genetic and antigenic diversity that has impeded the development of an effective vaccine using traditional methods. We are attempting to develop an AIDS vaccine by employing strategies that include structural biology and computational modelling, in an effort to develop immunogens capable of eliciting neutralizing antibodies of the requisite breadth and potency against circulating strains of HIV-1.     

The recombinant immunogen with high-density epitopes of ELDKWA and ELDEWA induced antibodies recognizing both epitopes on HIV-1 gp41

The high mutation rate of HIV-1 (human immunodeficiency virus-1) is a major obstacle to developing an effective vaccine. The mutation of ELDKWA-(aa669-674) to ELDEWA-epitope on HIV-1 gp41 caused the immune escape from neutralization by potent anti-HIV-1 human monoclonal antibody (mAb) 2F5. In this study, we suggested and evaluated a multi-epitope vaccine as a new strategy to develop HIV-1 vaccines. A glutathione S-transferase (GST) fusion protein (GST-K8E8) containing 8 copies of ELDKWA-and mutated ELDEWA-epitopes was constructed and used to immunize mice or rabbits. Analysis of the antisera (rAS3) induced by GST-K8E8 suggested that multi-epitope vaccine immunogen could raise antibodies in mice and rabbits against either the original ELDKWA-epitope or the mutated ELDEWA-epitope that resulted in immune escape. Briefly, ELDKWA-epitope-specific antibodies, directly purified from rAS3 by ELDKWA-epitope-peptide affinity chromatography, recognized either original gp41 protein (ELDKWA, rgp41K) or mutated gp41 (ELDEWA, rgp41E) in immunoblotting assay; in contrast, the existing ELDKWA-epitope antibodies recognized only rgp41K but not rgp41E, which were purified by ELDKWA-epitope-peptide affinity chromatography from rAS3 that were firstly completely pre-absorbed by ELDEWA-epitope-peptide affinity beads. And the same results were also observed when detecting the ELDEWA-epitope-specific antibodies in rAS3 by a means similar to the above. All the data presented here demonstrated that a high density multi-epitope vaccine could be an interesting strategy against HIV-1 mutation.     

Closing the door to human immunodeficiency virus

The pandemic of human immunodeficiency virus type one (HIV-1), the major etiologic agent of acquired immunodeficiency disease (AIDS), has led to over 33 million people living with the virus, among which 18 million are women and children. Until now, there is neither an effective vaccine nor a therapeutic cure despite over 30 years of efforts. Although the Thai RV144 vaccine trial has demonstrated an efficacy of 31.2%, an effective vaccine will likely rely on a breakthrough discovery of immunogens to elicit broadly reactive neutralizing antibodies, which may take years to achieve. Therefore, there is an urgency of exploring other prophylactic strategies. Recently, antiretroviral treatment as prevention is an exciting area of progress in HIV-1 research. Although effective, the implementation of such strategy faces great financial, political and social challenges in heavily affected regions such as developing countries where drug resistant viruses have already been found with growing incidence. Activating latently infected cells for therapeutic cure is another area of challenge. Since it is greatly difficult to eradicate HIV-1 after the establishment of viral latency, it is necessary to investigate strategies that may close the door to HIV-1. Here, we review studies on non-vaccine strategies in targeting viral entry, which may have critical implications for HIV-1 prevention.     

Immunogen design for HIV-1 and influenza

Vaccines provide the most cost effective defense against pathogens. Although vaccines have been designed for a number of viral diseases, a vaccine against HIV-1 still remains elusive. In contrast, while there are excellent influenza vaccines, these need to be changed every few years because of antigenic drift and shift. The recent discovery of a large number of broadly neutralizing antibodies (bNAbs) and structural characterization of the conserved epitopes targeted by them presents an opportunity for structure based HIV-1 and influenza A vaccine design. We discuss strategies to design immunogens either targeting a particular antigenic region or focusing on native structure stabilization. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.     

N-terminal residues of an HIV-1 gp41 membrane-proximal external region antigen influence broadly neutralizing 2F5-like antibodies

The Human immunodeficiency virus type 1(HIV-1) gp41 membrane proximal external region(MPER) is targeted by broadly neutralizing antibodies(e.g. 2F5, 4E10, Z13 e and m66.6), which makes this region a promising target for vaccine design. One strategy to elicit neutralizing antibodies against the MPER epitope is to design peptide immunogens mimicking neutralization structures. To probe 2F5-like neutralizing antibodies, two yeast-displayed antibody libraries from peripheral blood mononuclear cells from a HIV-1 patient were screened against the 2F5 epitope peptide SP62. Two 2F5-like antibodies were identified that specifically recognized SP62. However,these antibodies only weakly neutralized HIV-1 primary isolates. The epitopes recognized by these two 2F5-like antibodies include not only the 2F5 epitope(amino acids(aa) 662–667 in the MPER)but also several other residues(aa 652–655) locating at the N-terminus in SP62. Experimental results suggest that residues of SP62 adjacent to the 2F5 epitope influence the response of broadly neutralizing 2F5-like antibodies in vaccination. Our findings may aid the design of vaccine immunogens and development of therapeutics against HIV-1 infection.     

Induction of humoral immune responses following vaccination with envelope-containing, formaldehyde-treated, thermally inactivated human immunodeficiency virus type 1

The lack of success of subunit human immunodeficiency virus type 1 (HIV-1) vaccines to date suggests that multiple components or a complex virion structure may be required. We previously demonstrated retention of the major conformational epitopes of HIV-1 envelope following thermal treatment of virions. Moreover, antibody binding to some of these epitopes was significantly enhanced following thermal treatment. These included the neutralizing epitopes identified by monoclonal antibodies 1b12, 2G12, and 17b, some of which have been postulated to be partially occluded or cryptic in native virions. Based upon this finding, we hypothesized that a killed HIV vaccine could be derived to elicit protective humoral immune responses. Shedding of HIV-1 envelope has been described for some strains of HIV-1 and has been cited as one of the major impediments to developing an inactivated HIV-1 vaccine. In the present study, we demonstrate that treatment of virions with low-dose formaldehyde prior to thermal inactivation retains the association of viral envelope with virions. Moreover, mice and nonhuman primates vaccinated with formaldehyde-treated, thermally inactivated virions produce antibodies capable of neutralizing heterologous strains of HIV in peripheral blood mononuclear cell-, MAGI cell-, and U87-based infectivity assays. These data indicate that it is possible to create an immunogen by using formaldehyde-treated, thermally inactivated HIV-1 virions to induce neutralizing antibodies. These findings have broad implications for vaccine development.     

Structural Characterization of HIV gp41 with the Membrane-proximal External Region

Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development.     

Glycosylation as a tool for rational vaccine design

The discovery of broadly neutralizing antibodies that can neutralize multiple strains or subtypes of a pathogen has renewed interest in the development of broadly protective vaccines. To that end, there has been an interest in designing immunofocusing strategies to direct the immune response to specific, conserved regions on antigenic proteins. Modulation of glycosylation is one such immunofocusing strategy; extensive glycosylation is often exploited by pathogens for immune evasion. Masking epitopes on protein immunogens with “self” glycans can also shield the underlying protein surface from humoral immune surveillance. We review recent advances in applying glycosylation as an immunofocusing tool. We also highlight recent interesting work in the HIV-1 field involving the identification and elicitation of broadly neutralizing antibodies that incorporate glycans into their binding epitopes.     

Stabilizing HIV-1 envelope glycoprotein trimers to induce neutralizing antibodies

An effective HIV-1 vaccine probably will need to be able to induce broadly neutralizing HIV-1 antibodies (bNAbs) in order to be efficacious. The many bNAbs that have been isolated from HIV-1 infected patients illustrate that the human immune system is able to elicit this type of antibodies. The elucidation of the structure of the HIV-1 envelope glycoprotein (Env) trimer has further fueled the search for Env immunogens that induce bNAbs, but while native Env trimer mimetics are often capable of inducing strain-specific neutralizing antibodies (NAbs) against the parental virus, they have not yet induced potent bNAb responses. To improve the performance of Env trimer immunogens, researchers have studied the immune responses that Env trimers have induced in animals; they have evaluated how to best use Env trimers in various immunization regimens; and they have engineered increasingly stabilized Env trimer variants. Here, we review the different approaches that have been used to increase the stability of HIV-1 Env trimer immunogens with the aim of improving the induction of NAbs. In particular, we draw parallels between the various approaches to stabilize Env trimers and ones that have been used by nature in extremophile microorganisms in order to survive in extreme environmental conditions.     

10E8-like neutralizing antibodies against HIV-1 induced using a precisely designed conformational peptide as a vaccine prime

Recent studies have demonstrated that the membrane-proximal external region(MPER)of human immunodeficiency virus 1(HIV-1)glycoprotein 41 contains a series of epitopes for human monoclonal antibodies,including 2F5,Z13e1,4E10,and10E8,which were isolated from HIV-1-infected individuals and show broad neutralizing activities.This suggests that MPER is a good target for the development of effective HIV-1 vaccines.However,many studies have shown that it is difficult to induce antibodies with similar broad neutralizing activities using MPER-based peptide antigens.Here,we report that 10E8-like neutralizing antibodies with effective anti-HIV-1 activity were readily induced using a precisely designed conformational immunogenic peptide containing the 10E8-specific epitope.This immunogenic peptide(designated T10HE)contains a 15-mer MPER-derived 10E8-specific epitope fused to T-helper-cell epitopes from tetanus toxin(tt),which showed a significantly stabilized-helix structure after a series of modifications,including substitution with an(S)--(2-pentenyl)alanine containing an olefin-bearing tether and ruthenium-catalyzed olefin metathesis,compared with the unmodified T10E peptide.The stabilized-helix structure of T10HE did not affect its capacity to bind the 10E8 antibody,as evaluated with an enzyme linked immunosorbent assay(ELISA)and surface plasmon resonance binding assay(SPR assay).The efficacies of the T10HE and T10E epitope vaccines were evaluated after a standard vaccination procedure in which the experimental mice were primed with either the T10HE or T10E immunogen and boosted with HIV-1 JRFL pseudoviruses.Higher titers of 10E8-like antibodies were induced by T10HE than that by T10E.More importantly,the antibodies induced by T10HE showed enhanced antiviral potency against HIV-1 strains with both X4 and R5 tropism and a greater degree of broad neutralizing activity than the antibodies induced by T10E.These results indicate that a 10E8-epitope-based structure-specific peptide immunogen can elicit neutralizing antibodies when used as a vaccine prime.     

Detection of IgA-binding sites on human immunodeficiency virus type-1 envelope glycoproteins, Gp120 and Gp41

IgA has been supposed to play an important role in the prevention of HIV-1 infection. In this study, IgA-binding sites on gp120 and gp41 of HIV-1 envelope glycoproteins were analyzed using ELISA and overlapping synthetic peptides covering all of the gp120 and gp41 sites. IgA antibodies in plasma and saliva mainly bound to six and five sites on gp120 and gp41, respectively. Some of the IgA-binding sites differed from those of IgG-binding sites and the amount of IgA antibodies that bound to each site varied among samples. IgA antibodies in some plasma samples neutralized HIV-1 infection, and those IgA antibodies contained the antibodies which bound to the V3, C3 and ELDKWA sites. The results suggest that IgA antibodies which bind to certain sites on HIV-1 envelope glycoproteins may neutralize HIV-1 infection, presumably at mucosal sites where most IgA antibodies are produced. The induction of IgA antibodies that bind specific sites and neutralize HIV-1 infection at mucosal sites may be important in the development of a vaccine against HIV-1 infection.     

Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies

Design of an envelope-based immunogen capable of inducing a broadly neutralizing antibody response is thought to be key to the development of a protective HIV-1 vaccine. However, the broad diversity of viral variants and a limited ability to produce native envelope have hampered such design efforts. Here we describe adaptation of the yeast display system and use of a combinatorial protein engineering approach to permit directed evolution of HIV envelope variants. Because the intrinsic instability and complexity of this trimeric glycoprotein has greatly impeded the development of immunogens that properly represent the structure of native envelope, this platform addresses an essential need for methodologies with the capacity to rapidly engineer HIV spike proteins towards improved homogeneity, stability, and presentation of neutralizing epitopes. We report for the first time the display of a designed SOSIP gp140 on yeast, and the in vitro evolution of derivatives with greatly improved expression and binding to conformation-dependent antibodies. These efforts represent an initial and critical step toward the ability to rapidly engineer HIV-1 envelope immunogens via directed evolution.     

HIV中和抗体疫苗研究进展

由于HIV具有与其它微生物极为不同的生物学特点,HIV疫苗的研究面临着前所未有的困难和挑战。二十多年来,艾滋病疫苗研究主要采用了诱发中和抗体为主或细胞免疫为主两种策略,然而至今尚无实质性突破。诱发有效中和抗体一直是传统疫苗研发的重要策略,但HIV的高变异、多亚型等特点,使该策略在HIV疫苗研发中的应用成效甚微。近年来,一些具有广谱中和活性的HIV单抗的发现及其相应抗原表位的阐明,给HIV中和抗体疫苗的研究带来了新的希望。综合分析与评述这些进展,对于重新思考艾滋病疫苗和采用更好的策略进行艾滋病疫苗研究会有所帮助。     

Enhanced binding of antibodies to neutralization epitopes following thermal and chemical inactivation of human immunodeficiency virus type 1

Inactivation of viral particles is the basis for several vaccines currently in use. Initial attempts to use simian immunodeficiency virus to model a killed human immunodeficiency virus type 1 (HIV-1) vaccine were unsuccessful, and limited subsequent effort has been directed toward a systematic study of the requirements for a protective killed HIV-1 vaccine. Recent insights into HIV-1 virion and glycoprotein structure and neutralization epitopes led us to revisit whether inactivated HIV-1 particles could serve as the basis for an HIV-1 vaccine. Our results indicate that relatively simple processes involving thermal and chemical inactivation can inactivate HIV-1 by at least 7 logs. For some HIV-1 strains, significant amounts of envelope glycoproteins are retained in high-molecular-weight fractions. Importantly, we demonstrate retention of each of three conformation-dependent neutralization epitopes. Moreover, reactivity of monoclonal antibodies directed toward these epitopes is increased following treatment, suggesting greater exposure of the epitopes. In contrast, treatment of free envelope under the same conditions leads only to decreased antibody recognition. These inactivated virions can also be presented by human dendritic cells to direct a cell-mediated immune response in vitro. These data indicate that a systematic study of HIV-1 inactivation, gp120 retention, and epitope reactivity with conformation-specific neutralizing antibodies can provide important insights for the development of an effective killed HIV-1 vaccine.     

Solid-phase proteoliposomes containing human immunodeficiency virus envelope glycoproteins

The human immunodeficiency virus type 1 (HIV-1) exterior envelope glycoprotein gp120 mediates receptor binding and is the major target for neutralizing antibodies. A broadly neutralizing antibody response is likely to be a critical component of the immune response against HIV-1. Although antibodies against monomeric gp120 are readily elicited in immunized individuals, these antibodies are inefficient in neutralizing primary HIV-1 isolates. As a chronic pathogen, HIV-1 has evolved to avoid an optimal host response by a number of immune escape mechanisms. Monomeric gp120 that has dissociated from the functional trimer presents irrelevant epitopes that are not accessible on functional trimeric envelope glycoproteins. The resulting low level of antigenic cross-reactivity between monomeric gp120 and the functional spike may contribute to the inability of monomeric gp120 to elicit broadly neutralizing antibodies. Attempts to generate native, trimeric envelope glycoproteins as immunogens have been frustrated by both the lability of the gp120-gp41 interaction and the weak association between gp120 subunits. Here, we present solid-phase HIV-1 gp160DeltaCT (cytoplasmic tail-deleted) proteoliposomes (PLs) containing native, trimeric envelope glycoproteins in a physiologic membrane setting. We present data that indicate that the gp160DeltaCT glycoproteins on PLs are trimers and are recognized by several relevant conformational ligands in a manner similar to that for gp160DeltaCT oligomers expressed on the cell surface. The PLs represent a significant advance over present envelope glycoprotein formulations as candidate immunogens for HIV vaccine design and development.     

HIV-1壳体蛋白的结构及其病毒样颗粒疫苗

人类免疫缺陷病毒(HIV)的壳体蛋白(CA)在HIV病毒的组装和成熟过程中起着至关重要的作用。近年来,壳体蛋白的体外表达及其疫苗的研制成了HIV各项研究的焦点。由于壳体蛋白具有较好的的保守性,用其制得的疫苗也会提供比包膜蛋白更为广泛的免疫保护力。另外若将CA在体外表达成一个颗粒状结构,会增强其免疫原性,可以使疫苗发挥出更大的效力。