A potential peptide vaccine against two different strains of influenza virus isolated at intervals of about 10 years

Efforts to Improve the Seasonal Influenza Vaccine

Influenza viruses infect approximately 20% of the global population annually, resulting in hundreds of thousands of deaths. While there are Food and Drug Administration (FDA) approved antiviral drugs for combating the disease, vaccination remains the best strategy for preventing infection. Due to the rapid mutation rate of influenza viruses, vaccine formulations need to be updated every year to provide adequate protection. In recent years, a great amount of effort has been focused on the development of a universal vaccine capable of eliciting broadly protective immunity. While universal influenza vaccines clearly have the best potential to provide long-lasting protection against influenza viruses, the timeline for their development, as well as the true universality of protection they afford, remains uncertain. In an attempt to reduce influenza disease burden while universal vaccines are developed and tested, many groups are working on a variety of strategies to improve the efficacy of the standard seasonal vaccine. This review will highlight the different techniques and technologies that have been, or are being, developed to improve the seasonal vaccination efforts against influenza viruses.

Third-Kind Encounters in Biomedicine: Immunology Meets Mathematics and Informatics to Become Quantitative and Predictive

The understanding of the immune response is right now at the center of biomedical research. There are growing expectations that immune-based interventions will in the midterm provide new, personalized, and targeted therapeutic options for many severe and highly prevalent diseases, from aggressive cancers to infectious and autoimmune diseases. To this end, immunology should surpass its current descriptive and phenomenological nature, and become quantitative, and thereby predictive.Immunology is an ideal field for deploying the tools, methodologies, and philosophy of systems biology, an approach that combines quantitative experimental data, computational biology, and mathematical modeling. This is because, from an organism-wide perspective, the immunity is a biological system of systems, a paradigmatic instance of a multi-scale system. At the molecular scale, the critical phenotypic responses of immune cells are governed by large biochemical networks, enriched in nested regulatory motifs such as feedback and feedforward loops. This network complexity confers them the ability of highly nonlinear behavior, including remarkable examples of homeostasis, ultra-sensitivity, hysteresis, and bistability. Moving from the cellular level, different immune cell populations communicate with each other by direct physical contact or receiving and secreting signaling molecules such as cytokines. Moreover, the interaction of the immune system with its potential targets (e.g., pathogens or tumor cells) is far from simple, as it involves a number of attack and counterattack mechanisms that ultimately constitute a tightly regulated multi-feedback loop system. From a more practical perspective, this leads to the consequence that today's immunologists are facing an ever-increasing challenge of integrating massive quantities from multi-platforms.In this chapter, we support the idea that the analysis of the immune system demands the use of systems-level approaches to ensure the success in the search for more effective and personalized immune-based therapies.

Immunoinformatics: a brief review

A large volume of data relevant to immunology research has accumulated due to sequencing of genomes of the human and other model organisms. At the same time, huge amounts of clinical and epidemiologic data are being deposited in various scientific literature and clinical records. This accumulation of the information is like a goldmine for researchers looking for mechanisms of immune function and disease pathogenesis. Thus the need to handle this rapidly growing immunological resource has given rise to the field known as immunoinformatics. Immunoinformatics, otherwise known as computational immunology, is the interface between computer science and experimental immunology. It represents the use of computational methods and resources for the understanding of immunological information. It not only helps in dealing with huge amount of data but also plays a great role in defining new hypotheses related to immune responses. This chapter reviews classical immunology, different databases, and prediction tool. Further, it briefly describes applications of immunoinformatics in reverse vaccinology, immune system modeling, and cancer diagnosis and therapy. It also explores the idea of integrating immunoinformatics with systems biology for the development of personalized medicine. All these efforts save time and cost to a great extent.

Cross-protective peptide vaccine against influenza A viruses developed in HLA-A*2402 human immunity model

Background

The virus-specific cytotoxic T lymphocyte (CTL) induction is an important target for the development of a broadly protective human influenza vaccine, since most CTL epitopes are found on internal viral proteins and relatively conserved. In this study, the possibility of developing a strain/subtype-independent human influenza vaccine was explored by taking a bioinformatics approach to establish an immunogenic HLA-A24 restricted CTL epitope screening system in HLA-transgenic mice.

Methodology/Principal Findings

HLA-A24 restricted CTL epitope peptides derived from internal proteins of the H5N1 highly pathogenic avian influenza A virus were predicted by CTL epitope peptide prediction programs. Of 35 predicted peptides, six peptides exhibited remarkable cytotoxic activity in vivo. More than half of the mice which were subcutaneously vaccinated with the three most immunogenic and highly conserved epitopes among three different influenza A virus subtypes (H1N1, H3N2 and H5N1) survived lethal influenza virus challenge during both effector and memory CTL phases. Furthermore, mice that were intranasally vaccinated with these peptides remained free of clinical signs after lethal virus challenge during the effector phase.

Conclusions/Significance

This CTL epitope peptide selection system can be used as an effective tool for the development of a cross-protective human influenza vaccine. Furthermore this vaccine strategy can be applicable to the development of all intracellular pathogens vaccines to induce epitope-specific CTL that effectively eliminate infected cells.

Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines

It is generally assumed that amino acid mutations in the surface protein, hemagglutinin (HA), of influenza viruses allow these viruses to circumvent neutralization by antibodies induced during infection. However, empirical data on circulating influenza viruses show that certain amino acid changes to HA actually increase the efficiency of neutralization of the mutated virus by antibodies raised against the parent virus. Here, we suggest that this surprising increase in neutralization efficiency after HA mutation could reflect steric interference between antibodies. Specifically, if there is a steric competition for binding to HA by antibodies with different neutralization efficiencies, then a mutation that reduces the binding of antibodies with low neutralization efficiencies could increase overall viral neutralization. We use a mathematical model of virus-antibody interaction to elucidate the conditions under which amino acid mutations to HA could lead to an increase in viral neutralization. Using insights gained from the model, together with genetic and structural data, we predict that amino acid mutations to epitopes C and E of the HA of influenza A/H3N2 viruses could lead on average to an increase in the neutralization of the mutated viruses. We present data supporting this prediction and discuss the implications for the design of more effective vaccines against influenza viruses and other pathogens.

Peptides coupled to the surface of a kind of liposome protect infection of influenza viruses

In our previous study, OVA conjugated on the surface of a liposome, we termed Oleoyl liposome, which consisted of dioleoyl phosphatidyl choline, dioleoyl phosphatidyl ethanolamine, dioleoyl phosphatidyl glycerol acid and cholesterol in a 4:3:7:2 molar ratio, induced OVA-specific IgG antibody production but not OVA-specific IgE antibody production that is detrimental to the host. Furthermore, OVA(257-264)-Oleoyl liposome elicited CTL responses in the presence of CpG and rejected E.G7 tumors in mice. In this study we tested whether a peptide-Oleoyl liposome conjugates are capable of inducing protection against viral growth. Subcutaneous inoculation of NP(366-374)-Oleoyl liposome with CpG inhibited growth of influenza viruses in lungs of mice. Thus, surface-linked liposomal peptide might serve as an effective vaccine without detrimental effects in the presence of immune potentiators.

Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201

A method has been developed for prediction of binding affinities between proteins and peptides. We exemplify the method through its application to binding predictions of peptides with affinity to major histocompatibility complex class I molecule HLA-A*0201. The method is named "additive" because it is based on the assumption that the binding affinity of a peptide could be presented as a sum of the contributions of the amino acids at each position and the interactions between them. The amino acid contributions and the contributions of the interactions between adjacent side chains and every second side chain were derived using a partial least squares (PLS) statistical methodology using a training set of 420 experimental IC50 values. The predictive power of the method was assessed using rigorous cross-validation and using an independent test set of 89 peptides. The mean value of the residuals between the experimental and predicted pIC50 values was 0.508 for this test set. The additive method was implemented in a program for rapid T-cell epitope search. It is universal and can be applied to any peptide-protein interaction where binding data is known.

Peptide dendrimers: applications and synthesis

Peptide dendrimers are radial or wedge-like branched macromolecules consisting of a peptidyl branching core and/or covalently attached surface functional units. The multimeric nature of these constructs, the unambiguous composition and ease of production make this type of dendrimer well suited to various biotechnological and biochemical applications. Applications include use as biomedical diagnostic reagents, protein mimetics, anticancer and antiviral agents, vaccines and drug and gene delivery vehicles. This review focuses on the different types of peptide dendrimers currently in use and the synthetic methods commonly employed to generate peptide dendrimers ranging from stepwise solid-phase synthesis to chemoselective and orthogonal ligation.

Nasal delivery of epitope based vaccines

Essentially all of the currently available vaccines are based on the use of inactivated or live-attenuated pathogens. However, these vaccines have several shortcomings, such as difficulties of in vitro culturing, biohazard risks, as well as loss of efficacy due to the genetic variations seen in many viruses. These problems may potentially be solved by immunising with epitope-based vaccines consisting of rationally designed protective epitopes, appropriately presented and easy to deliver, which are capable of stimulating effective B-cell, T-cell and cytotoxic immune responses whilst avoiding potentially hazardous and undesirable effects. Furthermore, the use of a mixture of defined epitopes could lead to an effective broad range immune response which has the potential to overcome both strain specificity of the pathogen and the MHC restriction of the host. Epitope-based vaccines can be designed to involve the use of synthetic materials that can be available in unlimited quantities and posing no biohazard. Other approaches include the use of naked DNA or recombinant viruses or bacteria expressing the epitopes. An important objective in the development of such vaccines is that they should be effective when delivered via the mucosal route and effective in the presence of maternal antibodies. In this review, we present examples of the use of various epitope-based vaccine constructs, focussing particularly upon their intranasal delivery to the immune system.

Amelioration of experimental autoimmune uveoretinitis by pretreatment with a pathogenic peptide in liposome and anti-CD40 ligand monoclonal antibody

We have defined a peptide K2 (ADKDVVVLTSSRTGGV) that corresponds to residues 201-216 of bovine interphotoreceptor retinoid-binding protein and induces experimental autoimmune uveoretinitis (EAU)4 in H-2Ak-carrying mice (H-2Ak mice). In this study, we attempted to ameliorate EAU in the H-2Ak mice without nonspecific suppression of T cell responses. Preceding s.c. administration of liposomes including K2 (liposomal K2) specifically inhibited subsequent generation of T cell response to K2. The same result was obtained with a combination of OVA323-339 peptide and the OVA-specific TCR-transgenic T cells. It was suggested that the inhibition was mainly attributed to peripheral anergy induction of T cells specific for the peptide Ag, although specific cell death might also be involved in the inhibition. Pretreatment with liposomal K2 also considerably abolished IFN-gamma production but not IL-4 production. The specific inhibitory effect of the pretreatment with liposomal peptide was augmented by a simultaneous administration of anti-CD40 ligand (anti-CD40L) mAb. Moreover, it was shown that the pretreatment with liposomal K2 reduced both the incidence and severity of the subsequent K2-induced EAU, and the simultaneous administration of anti-CD40L mAb augmented this preventive effect by liposomal K2. Our findings demonstrate that the s.c. administration of liposomal pathogenic peptide and anti-CD40L mAb can be applied to preventing autoimmune diseases without detrimental nonspecific suppression of T cell responses.

Effective priming of cytotoxic T lymphocyte precursors by subcutaneous administration of peptide antigens in liposomes accompanied by anti-CD40 and anti-CTLA-4 antibodies

Recently it has been shown that modulation of CD40 molecules on antigen (Ag) carrying dendritic cells (DC) can bypass T cell help, resulting in priming cytotoxic T lymphocytes (CTL) specific for the Ag. In the present study we attempted to prime peptide Ag-specific CTL by a new method in which a peptide Ag in liposome (liposomal peptide), consisting of phosphatidylserine and phosphatidylcholine (3:7), was administrated subcutaneously with anti-CD40 and/or CTLA-4 monoclonal antibodies (mAb) to mice. We found that the subcutaneous administration of the liposomal peptide with both anti-CD40 and anti-CTLA-4 mAb enhanced CTL responses comparing with those induced by the liposomal peptide alone or the liposomal peptide plus each mAb. It was shown that liposomes were critical for induction of the CTL activity. Flow cytometry analysis of a peptide-bearing DC in lymph nodes (LN) and measurement of serum IL-12 indicated that anti-CD40 mAb promoted migration of DC to the LN, where DC might differentiate and acquire ability of priming CTL. These findings provide a possibility that our procedure is applicable to cancer patients.

Prevention of infection of influenza virus in DQ6 mice, a human model, by a peptide vaccine prepared according to the cassette theory

We proposed a strategy (cassette theory) in which non-binding peptides for murine major histocompatibility complex (MHC) class II molecules are introduced into a MHC-binding component to render the resultant hybrid peptides bound to the MHC and thus immunogenic in animals carrying the relevant MHC. It was shown that 46F/HA127-133/54A(18mer) peptide which was prepared by introducing hemagglutinin (HA)127-133 of influenza virus into the H-2Ab binding component induced significant T cell responses and antibodies (Ab) specific for HA127-133 in H-2Ab mice. Further we found that the H-2Ab binding component had a supermotif for human class II molecules (i.e. HLA-DQ6). In the present study, a new peptide vaccine, H3-H3, was prepared by combining 46F/HA127-133/54A(18mer) as a carrier and HA127-133 attached to the C terminus of 46F/HA127-133/54A(18mer) as a hapten and the effect of vaccine was examined in DQ6 mice which carry HLA-DQ6 alone as MHC class II molecules and thus may be regarded as a model of the DQ6 positive individuals. Since 46F/HA127-133/ 54A(18mer) induced merely Ab against HA127-133, it was assumed that H3-H3 induced mainly HA127-133 specific Ab in DQ6 mice without undesirable Ab production against the carrier. Indeed, H3-H3 elicited T cell responses and induced HA127-133 specific Ab in DQ6 mice. Furthermore, administration of H3-H3 inhibited growth of influenza virus until 9 weeks after the last immunization in DQ6 mice.

A novel influenza subunit vaccine composed of liposome-encapsulated haemagglutinin/neuraminidase and IL-2 or GM-CSF. II. Induction of TH1 and TH2 responses in mice

This study was aimed at analyzing, in parallel, the humoral and cellular immune responses elicited in mice immunized with liposomal influenza A (Shangdong/9/93) subunit vaccines composed of haemagglutinin/neuraminidase (H3N2) and IL-2 or GM-CSF. Recently, we reported that such vaccines evoke a more rapid, stronger and longer-lasting (over 1 year) humoral response, as well as protective immunity against viral infection, following a single administration, as compared with the response induced by the free antigen given alone or together with soluble cytokines. In the present study, BALB/C mice were immunized once, i.p., s.c., i.m. or i.n., with nonliposomal or liposomal vaccines and the humoral (antibody titer and isotypes) and cellular (DTH, cytotoxicity, cytokine production) responses were assessed at various times (2-56 weeks). The main findings were: (a) the combined liposomal vaccines consisting of encapsulated antigen and encapsulated cytokine, but not the free antigen, elicited a high titer of serum IgG1, IgG2a, IgG3 and IgM antibodies; (b) the combined liposomal vaccines were efficient following administration by the various routes, and induced a local (in lung) IgA response in i.n. vaccinated mice; (c) the liposomal vaccines triggered DTH and cytotoxic responses, as well as cytokine (mainly IL-4) production. Together, these and other findings indicate that our cytokine-supported liposomal influenza vaccines efficiently stimulate both Th1 and Th2 responses and that such vaccines may be more potent in high-risk groups than the currently used subunit vaccines.

Two complementary methods for predicting peptides binding major histocompatibility complex molecules

Peptides that bind to major histocompatibility complex products (MHC) are known to exhibit certain sequence motifs which, though common, are neither necessary nor sufficient for binding: MHCs bind certain peptides that do not have the characteristic motifs and only about 30% of the peptides having the required motif, bind. In order to develop and test more accurate methods we measured the binding affinity of 463 nonamer peptides to HLA-A2.1. We describe two methods for predicting whether a given peptide will bind to an MHC and apply them to these peptides. One method is based on simulating a neural network and another, called the polynomial method, is based on statistical parameter estimation assuming independent binding of the side-chains of residues. We compare these methods with each other and with standard motif-based methods. The two methods are complementary, and both are superior to sequence motifs. The neural net is superior to simple motif searches in eliminating false positives. Its behavior can be coarsely tuned to the strength of binding desired and it is extendable in a straightforward fashion to other alleles. The polynomial method, on the other hand, has high sensitivity and is a superior method for eliminating false negatives. We discuss the validity of the independent binding assumption in such predictions.

ZP3 peptide vaccine that induces antibody and reversible infertility without autoimmune oophoritis

Autoantibodies to ZP3, a major glycoprotein of the zona pellucida (ZP) with sperm receptor function, can block sperm/oocyte interaction. However, only mice of certain major histocompatibility complex (MHC) haplotype respond to the ZP3 peptide. Moreover, ZP3-specific T cells can mediate ovarian autoimmune disease. A chimeric peptide has been designed that induces antibody to native ZP3 regardless of the MHC haplotype of the inbred mice tested. This results in reduction in fertility that is reversible. Infertility correlates well with ZP antibody titer, and the mice do not develop concomitant autoimmune oophoritis. The vaccine contains (1) a promiscuous foreign T-cell peptide capable of eliciting a T-cell response regardless of the animals' MHC haplotype, and (2) a modified native B-cell peptide of ZP3.