HIV‐1: From escapism to conservatism (2011)

In June this year, it was 30 years since the identification of the first AIDS patient (see the review in this issue 1). Despite rapid responses by scientists and doctors to understand this disease in both clinical and experimental systems 2, 3, human immunodeficiency virus type 1 (HIV-1), the causative agent of AIDS (Fig. 1), continues to feature among world's three major killers destroying millions of lives, families and communities. More than 30 drugs have been developed just for HIV-1 and there have been three successful trials showing their impressive preventive potential. However, because of the drug unavailability, particularly in resource poor settings, side effects and potential development of resistance, the best hope for a profound fall in the incidence of HIV-1 infection remains the development of an effective prophylactic HIV-1 vaccine. Here, we discuss T-cell vaccine designs mainly, briefly mentioning antibody vaccines. HIV © PhotoDisc, Inc. Even if a vaccine that actively stimulates broadly neutralizing antibodies (bNAbs) can be made 4, it will be hard to stop some HIV-1 infection occurring (e.g. through cell–cell transmission) and T-cell-mediated immune responses to control infection will be required. T cells function by killing HIV-1-infected cells and producing soluble factors that can directly and indirectly control HIV-1 spread. While T cells cannot prevent the transmitted virus from infecting host cells, potent vaccine-induced HIV-1-specific T-cell responses could increase the dose of incoming virus necessary to establish infection (i.e. decrease acquisition) 5, limit the extent of viral replication during primary viremia (i.e. reduce tissue damage), lower the virus load at set point (i.e. reduce further virus transmission) and slow the rate of CD4+ T-cell decline (i.e. delay the development of AIDS). The simian immunodeficiency virus/macaque challenge model strongly supports this view, showing that potent T-cell responses alone can lower virus load and delay the development of AIDS 6-8. Thus, ideally, a successful HIV-1 vaccine will induce both T-cell and antibody responses; however, an effective T- or B-cell vaccine alone is nonetheless likely to impact the epidemic 9. Scientists developing HIV-1 vaccines face a long list of challenges. Although these differ for the induction of effective T-cell responses in comparison with induction of the desired bNAb specificity by active immunization, one major hurdle is common, namely the extreme HIV-1 variability. The main HIV-1 group has diversified into 15 major clades, subclades and interclade recombinant circulating forms, whereby individual HIV-1 variants, even within clades, may differ by up to 20% of their amino acid sequence, which is more than enough to severely impair broad T-cell and antibody recognition. CD8+ T-cell recognition of epitopes is usually highly sensitive to even a single amino acid deviation from the well-recognized sequence and this decreases T-cell recognition efficacy. Thus, a successful vaccine has to effectively recognize diverse infecting HIV-1 strains circulating in the population and then must deal with ongoing virus escape in infected individuals. Although in acute HIV-1 infection, the founding virus is usually single, the first T-cell responses tend to focus on immunodominant, but highly variable epitopes, in which mutations are selected very rapidly, escaping the early T-cell responses. NAbs develop much later in infection after the damage to the immune system is already done. HIV-1 has an enormous capacity to change. Some HIV-1 proteins such as the envelope are more variable than e.g. the internal structural proteins. On a sub-molecular level, some protein regions have to remain more-or-less constant to maintain their structural or biological functions and, therefore, even HIV-1 has its Achilles heel and this can be exploited. Focusing the vaccine-elicited responses on the functionally conserved regions of the HIV-1 proteome has a number of advantages. First, conserved regions are common to the diverse virus strains and clades to which vaccines are exposed. Second, targeting the conserved regions reduces the chance of virus escape in infected individuals. If escape mutations do occur, and some have been documented in conserved regions 10, they may often decrease virus fitness as shown e.g. for a B57-restricted epitope 11, or may require compensating mutation(s) as in the case of a B27-restricted Gag epitope 12. Therefore, escape mutations in the conserved regions may be good for patient's clinical prognosis or may be very delayed. Third, T-cell immunogens based on the functionally conserved parts of HIV-1 proteins redirect the naturally induced hierarchy of epitope responses, which is non-protective, towards invariable regions, which are arguably more likely to be protective. Finally, conserved immunogens can be designed as a simple single insert, representative of the major global clades A, B, C, and D equally. Therefore, vaccines based on the conserved regions of the HIV-1 proteome can be tested and potentially deployed in Europe, America, Asia, and Africa; they are universal. The first conserved region vaccine entered clinical evaluation in HIV-1 seronegative volunteers in Oxford, UK, and the results are expected in summer 2012. Most initial vaccine strategies focused on the breadth, i.e. the number of different epitopes of the HIV-1 proteome recognized by vaccine-induced responses, rather than the depth defined as the number of variants of the same epitopes. Therefore, early vaccines often incorporated into their formulations almost a whole set of virus proteins. The rationale behind this was that, if a multiplicity of epitopes were recognized at the same time, this would prevent HIV-1 from changing all of these epitopes at the same time and escaping immune surveillance. An example of such a single clade vaccine is MRKAd5 developed by the Merck Research Laboratories, which showed no efficacy in the first T-cell vaccine STEP trial in 2007 13, 14. When the power of the virus variability became more appreciated and respected, many vaccine designs mixed variants of the same protein derived from several different HIV-1 clades into a single formulation. One such vaccine is currently in a recently expanded phase IIb proof-of-concept trial designated the HIV Vaccine Trials Network (HVTN) protocol 505 15. More advanced T-cell-based vaccine strategies have taken full advantage of the Los Alamos National Laboratory (LANL) HIV Sequence Database, which has the most complete data set of known HIV-1 isolates. The first in silico approach that emerged computed centralized sequences 16. This approach uses either consensus (average) or centre-of-phylogenetic tree whole protein sequences or extrapolates individual amino acid positions in the whole proteins to common clade or group ancestors. This captures the intraclade variation, but is likely to be too stretched to comprehensively cover the whole main group of HIV-1 variants. The best coverage of the ‘non-conserved’ strategies computes mosaic proteins, which are artificial sequences assembled in silico using an iterative algorithm 17. Known 9-amino acid stretches were chosen because this is the most typical length of an epitope recognized by CD8+ T killer cells and by computing mosaic proteins the coverage of all common variants of these sequences is maximized. For example, a tetravalent mosaic protein of Gag optimized on the main group sequences covers about 74% of the main group Gag-derived 9-mers as a perfect match. Both computed designs described are supported by a strong rationale; nevertheless, they do not refocus the immune responses away from the dominant, hypervariable regions towards the subdominant but invariant regions of HIV-1 18, 19. This means that the induced T-cell responses, although increased in depth, are just as likely to focus on variable regions and this opens the possibility of selecting novel escape variants not yet included in the LANL database. Recent deep sequencing of natural T-cell escape mutations showed that a very large number of alternative amino acids were generated by mutation during infection and ‘tested’ in these variable epitope positions 20. In essence, perhaps the best solution to a T-cell vaccine immunogen is one that consists of conserved regions made of mosaic sequences. The first mosaic vaccine is scheduled to enter clinical evaluation in year 2012. Even the most conserved regions of the HIV-1 proteome are not immunologically inert. By inspecting the LANL HIV-1 database, it can be seen that conserved regions contain their fair share of CD8+ T-cell epitopes, which are proportional to their amino acid length. These epitopes were identified mostly in chronically infected individuals, who had mounted T-cell responses against them. Moreover, preliminary immunogenicity results from the first trials of the conserved vaccines show encouraging immunogenicity. Nevertheless, as with any approach, vaccines based on the conserved regions have their theoretical caveats. First, conserved immunogens are chimeric proteins assembled from protein sub-regions and, as such, have sequence junctions where the sub-regions meet. These junctions may create novel irrelevant epitopes (not present in HIV-1), which could, for certain HLAs, be immunodominant and suppress induction of protective responses. However, based on the likelihood of creating such immunodominant interfering junctional epitopes, these will almost certainly be the exception rather than the rule. Second, CD4+ T cells, the main natural target cells for HIV-1 replication, do not have co-stimulatory molecules on their surface and, therefore, are not potent primers of T-cell responses. Thus, in natural HIV-1 infection, many or most T-cell responses are primed either by direct infection of ‘professional’ antigen-presenting cells or through cross-priming, for instance via the uptake of HIV-1-infected apoptotic cell debris by ‘professional’ antigen-presenting cells. While it is known that most immunodominant epitopes are expressed on HIV-1-infected cells, this has not been explored in great detail for subdominant epitopes such as those derived from the HIV-1 conserved regions. Thus, it is not guaranteed that HIV-1-infected cells express conserved epitopes on their surface in sufficient amounts for effective and timely killing by cytotoxic T cells, i.e. before the infected cells produce HIV-1 progeny, which is key for the success of conserved T-cell vaccines (Fig. 2). Both of these caveats are being investigated in the on-going clinical trials of the conserved vaccines by e.g. in vitro virus suppression assays utilising vaccine-induced T-cell effectors 21. Are subdominant epitopes from conserved regions of the HIV-1 proteome presented efficiently on the surface of HIV-1-infected cells? The strategy for controlling HIV-1 by the use of conserved T-cell epitopes has been proposed on several occasions 22-24. However, an actual T-cell vaccine employing conserved regions (rather than epitopes) of HIV-1, thus preserving the natural epitope adjacent sequences and also the possibility of inducing responses to as yet unidentified epitopes, was first reported by Letourneau et al., who employed the 14 most conserved regions of the proteome as 27- to 128-amino acid-long consensus sequences alternating the four major main global clades A, B, C, and D 25. At about the same time, such an approach was theoretically proposed by Rolland et al., who suggested the use of 45 conserved elements (CEs) at least 8 amino acids long that fulfilled stringent conservation criteria 26. Since then, there has been a flurry of papers addressing and discussing various aspects of universal vaccines based on conserved regions of HIV-1, including for example: conserved region vaccines being tested in rhesus macaques and found to be highly immunogenic 27; proposal of a universal peptide vaccine based on conserved regions of HIV-1 28; recognition of conserved and variable CD8+ T-cell epitopes with similar probabilities during both primary and chronic infections, whereby the conserved epitopes generally elicited subdominant responses 29; detection of an association between responses to conserved T-cell epitopes and lower virus loads 30; skewing of vaccine-elicited T-cell responses away from more conserved epitopes to the more variable and therefore possibly less protective epitopes, which did not match the infecting viruses, as detected in the failed STEP trial 31; a novel analysis of controllers who durably control HIV-1 without medications that revealed preferential targeting of a conserved sector in Gag and concluded that targeting regions with higher order evolutionary constraints provides a novel approach to immunogen design 32; Thus, support for T-cell vaccine strategies employing conserved regions of the HIV-1 proteome is growing. Many pathogens use antigenic variability of the most immunogenic regions on their surface to avoid host antibody-based defences. Thus, antibody-inducing vaccines have a much longer tradition in focusing on conserved regions 33. Indeed, even the most variable protein, Env, of HIV-1 has invariable regions, of which the most conserved is the CD4 receptor-binding site 34. Recently, there has been tremendous progress in understanding the mechanisms underlying potent and broad HIV-1 neutralization 35, 36. The roadblock of efficiently inducing such specificity by active vaccination remains, but conserved regions are once again at the centre of attention. This article has mainly concentrated on the theoretical arguments for and against the various HIV-1 immunogen platforms currently under evaluation; it provides only limited experimental evidence because this is only just starting to emerge. Vaccine success will depend significantly, but not exclusively on immunogens; it will also be critical to factor in how these immunogens are presented to the immune system, i.e. the choice of vaccine vectors and vector combinations, adjuvantation and routes of delivery 37. Which vaccine strategy is the best can be only decided by protection of humans against HIV-1 infection and/or AIDS and this, in turn, can only be answered in efficacy trials. These are expensive, but highly informative. Moreover, the very last one, RV144 38, even provided a moderate reason for optimism. Last but not least, vaccines will not be discovered without continued financial and political support, new scientific discoveries and human will and persistence. World AIDS day (http://www.worldaidsday.org/) on 1 December offers the perfect opportunity to ensure that such issues are highlighted globally.