POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties

MOTIVATION: Both modeling of antigen-processing pathway including major histocompatibility complex (MHC) binding and immunogenicity prediction of those MHC-binding peptides are essential to develop a computer-aided system of peptide-based vaccine design that is one goal of immunoinformatics. Numerous studies have dealt with modeling the immunogenic pathway but not the intractable problem of immunogenicity prediction due to complex effects of many intrinsic and extrinsic factors. Moderate affinity of the MHC-peptide complex is essential to induce immune responses, but the relationship between the affinity and peptide immunogenicity is too weak to use for predicting immunogenicity. This study focuses on mining informative physicochemical properties from known experimental immunogenicity data to understand immune responses and predict immunogenicity of MHC-binding peptides accurately. RESULTS: This study proposes a computational method to mine a feature set of informative physicochemical properties from MHC class I binding peptides to design a support vector machine (SVM) based system (named POPI) for the prediction of peptide immunogenicity. High performance of POPI arises mainly from an inheritable bi-objective genetic algorithm, which aims to automatically determine the best number m out of 531 physicochemical properties, identify these m properties and tune SVM parameters simultaneously. The dataset consisting of 428 human MHC class I binding peptides belonging to four classes of immunogenicity was established from MHCPEP, a database of MHC-binding peptides (Brusic et al., 1998). POPI, utilizing the m = 23 selected properties, performs well with the accuracy of 64.72% using leave-one-out cross-validation, compared with two sequence alignment-based prediction methods ALIGN (54.91%) and PSI-BLAST (53.23%). POPI is the first computational system for prediction of peptide immunogenicity based on physicochemical properties. AVAILABILITY: A web server for prediction of peptide immunogenicity (POPI) and the used dataset of MHC class I binding peptides (PEPMHCI) are available at http://iclab.life.nctu.edu.tw/POPI     

Reverse vaccinology

Biochemical, serological and microbiological methods have been used to dissect pathogens and identify the components useful for vaccine development. Although successful in many cases, this approach is time-consuming and fails when the pathogens cannot be cultivated in vitro, or when the most abundant antigens are variable in sequence. Now genomic approaches allow prediction of all antigens, independent of their abundance and immunogenicity during infection, without the need to grow the pathogen in vitro. This allows vaccine development using non-conventional antigens and exploiting non-conventional arms of the immune system. Many vaccines impossible to develop so far will become a reality. Since the process of vaccine discovery starts in silico using the genetic information rather than the pathogen itself, this novel process can be named reverse vaccinology.     

猪流行性腹泻mRNA疫苗的制备与免疫原性评价

猪流行性腹泻(porcine epidemic diarrhea,PED)是一种可引起仔猪高致死率的传染性疾病,尽管已有灭活疫苗和减毒活疫苗上市,但由于病毒变异频繁导致保护效力欠佳,发病率依然居高不下。本研究首次制备了PED mRNA候选疫苗,并在小鼠和妊娠母猪上评价了其免疫原性,证明了基于病毒受体结合区异源二聚体的mRNA候选疫苗具有良好的免疫原性,可在小鼠上高效诱导体液和细胞免疫应答,单次免疫血清中和抗体滴度达到1:300以上,并在妊娠母猪上诱导了与灭活疫苗相近的中和抗体水平,实现了100%抗体转阳。本研究为PED mRNA疫苗的进一步产业化奠定了基础。     

转基因植物作为生物反应器生产口蹄疫疫苗的研究进展

利用转基因植物作为生物反应器表达重组蛋白,生产外源蛋白质作为动物疫苗是一个很有吸引力的廉价生产系统,它有可能代替生产成本较高的传统疫苗的发酵生产系统。通过口蹄疫病毒VP1结构蛋白基因在转基因植物中的表达,口蹄疫疫苗已在植物中产生。在植物中生产的抗原能够保持其自身的免疫原性。本文简要综述了近十年来用转基因植物作为生物反应器生产口蹄疫疫苗的研究进展、特点及其应用前景 。     

脂质体、免疫刺激复合物和壳聚糖作为黏膜免疫载体的研究现状

查阅国内外文献,采用整理归纳、引用和分析的方法,概述了鼻黏膜免疫载体材料脂质体、免疫刺激复合物和壳聚糖的生物学特性及其在气溶胶疫苗领域的应用。脂质体、免疫刺激复合物和壳聚糖作为气溶胶疫苗鼻黏膜免疫的载体,能够增强疫苗的免疫原性,提高机体的体液免疫和细胞免疫水平,因此,可作为疫苗抗原激发特异免疫应答的生物材料。     

Evaluation of a guinea pig model to assess interference in the immunogenicity of different components of a combination vaccine comprising diphtheria, tetanus and acellular pertussis (DTaP) vaccine and haemophilus influenzae type b capsular polysaccharide conjugate vaccine.

A guinea pig model to assess the immunogenicity of a combination vaccine containing diphtheria, tetanus and acellular pertussis (DTaP) vaccine and Haemophilus influenzae type b (Hib) capsular polysaccharide conjugated to tetanus toxoid (HibT) was evaluated comparatively with the mouse immunogenicity test to study the effect of combining these antigens on the immunogenicity of various components. The immunogenicity test in mice was performed by subcutaneous injection of groups of 10 animals twice at an interval of four weeks with 1/10 of a single human dose of various formulations of combination vaccines, DTaP or HibT vaccine. The animals were bled at 4 and 6 weeks and IgG or total antibodies to various components were determined by ELISA or RIA. The guinea pig immunogenicity model included groups of animals injected subcutaneously twice at an interval of six weeks with 1.5 times the single human dose of various formulations. The animals were bled at 4, 6 and 8 weeks and serum samples were tested for antibodies to various components by ELISA, RIA and/or neutralization tests. Additionally, potency of tetanus and diphtheria components was assessed as per the US Food and Drug Administration's regulations. Aluminium phosphate (AIPO(4)) adsorbed HibT vaccine or HibT as a combination with AIPO(4)adsorbed DTaP vaccine showed significant increases in IgG antibodies to tetanus toxin in mice as well increased tetanus antitoxin levels in guinea pigs as compared to soluble HibT vaccine. In general, combining DTaP and HibT vaccines did not affect the antibody levels to tetanus and diphtheria toxoids whereas DTaP-HibT combination vaccine elicited significantly lower IgG antibodies to pertussis toxin and filamentous haemagglutinin than DTaP vaccine alone, particularly after first injection. Mice showed similar Hib antibody responses for the combination and HibT alone whereas guinea pigs consistently showed lower anamnestic responses to Hib for combination formulations than for HibT alone. Reducing the amount of HibT and/or tetanus toxoid in the combination formulations reduced this suppression of Hib antibody response in guinea pigs. Suppression of Hib antibody response in combination vaccines has also been reported from recent clinical trials. Based on the results from this study, it appears that the guinea pig model may be able to predict the human response to various components of combination vaccines.     

Importance of the degree of antigen polymerization by detoxification in modulating the immunogenicity of acellular pertussis vaccine

For the acellular pertussis vaccine with a high immunogenicity, the concentration, composition and characteristics of acellular pertussis antigens are the crucial points to be considered. Nevertheless, it has not been proved yet whether or not the polymerization degree, one of the characteristics of formalin-detoxified acellular pertussis antigens, has an influence on vaccine potency. Thus, in the present study, the correlations among detoxification conditions of acellular pertussis bulks, their polymerization degrees and their immunogenicities were examined. In addition, the relative importance of pertussis toxoid in vaccine immunogenicity was also investigated. Results show that a lower lysine concentration during detoxification induces highly-polymerized antigens, the immunogenicity has a great dependency on the polymerization degree of antigens, and also pertussis toxoid has a relatively stronger influence on the immunogenicity than other antigens. Accordingly, in the aspect of the potency of detoxified acellular pertussis vaccine, it can be demonstrated that the polymerization of antigens and its degree are the major factors affecting the immunogenicity along with a relatively high content of pertussis toxoid.     

肽疫苗的研究进展

肽疫苗可分为3大类,即抗病毒相关肽疫苗、抗肿瘤相关肽疫苗、抗细菌及寄生虫感染的肽疫苗。肽疫苗具有安全、廉价、特异性强、易于保存和应用等特点。本主要介绍有关肽疫苗的设计、提高免疫原性及体内的稳定性、复合肽疫苗、临床评价等方面的研究和应用进展。     

Immunogenicity of self-associated aggregates and chemically cross-linked conjugates of the 42 kDa Plasmodium falciparum merozoite surface protein-1

Self-associated protein aggregates or cross-linked protein conjugates are, in general, more immunogenic than oligomeric or monomeric forms. In particular, the immunogenicity in mice of a recombinant malaria transmission blocking vaccine candidate, the ookinete specific Plasmodium falciparum 25 kDa protein (Pfs25), was increased more than 1000-fold when evaluated as a chemical cross-linked protein-protein conjugate as compared to a formulated monomer. Whether alternative approaches using protein complexes improve the immunogenicity of other recombinant malaria vaccine candidates is worth assessing. In this work, the immunogenicity of the recombinant 42 kDa processed form of the P. falciparum merozoite surface protein 1 (MSP1(42)) was evaluated as a self-associated, non-covalent aggregate and as a chemical cross-linked protein-protein conjugate to ExoProtein A, which is a recombinant detoxified form of Pseudomonas aeruginosa exotoxin A. MSP1(42) conjugates were prepared and characterized biochemically and biophysically to determine their molar mass in solution and stoichiometry, when relevant. The immunogenicity of the MSP1(42) self-associated aggregates, cross-linked chemical conjugates and monomers were compared in BALB/c mice after adsorption to aluminum hydroxide adjuvant, and in one instance in association with the TLR9 agonist CPG7909 with an aluminum hydroxide formulation. Antibody titers were assessed by ELISA. Unlike observations made for Pfs25, no significant enhancement in MSP1(42) specific antibody titers was observed for any conjugate as compared to the formulated monomer or dimer, except for the addition of the TLR9 agonist CPG7909. Clearly, enhancing the immunogenicity of a recombinant protein vaccine candidate by the formation of protein complexes must be established on an empirical basis.     

The Development of Multi-epitope Vaccines: Epitope Identification, Vaccine Design and Clinical Evaluation

We have developed efficient methods for epitope identification and vaccine design. Our process for epitope selection based on the combined use of motif analyses, binding assays and immunogenicity evaluations is described. We also describe how the projected population coverage and vaccine design can be optimized. Finally, it is discussed how vaccine potency is evaluated by immunogenicity and antigenicity assays.     

The Effect of Human Factor H on Immunogenicity of Meningococcal Native Outer Membrane Vesicle Vaccines with Over-Expressed Factor H Binding Protein

The binding of human complement inhibitors to vaccine antigens in vivo could diminish their immunogenicity. A meningococcal ligand for the complement down-regulator, factor H (fH), is fH-binding protein (fHbp), which is specific for human fH. Vaccines containing recombinant fHbp or native outer membrane vesicles (NOMV) from mutant strains with over-expressed fHbp are in clinical development. In a previous study in transgenic mice, the presence of human fH impaired the immunogenicity of a recombinant fHbp vaccine. In the present study, we prepared two NOMV vaccines from mutant group B strains with over-expressed wild-type fHbp or an R41S mutant fHbp with no detectable fH binding. In wild-type mice in which mouse fH did not bind to fHbp in either vaccine, the NOMV vaccine with wild-type fHbp elicited 2-fold higher serum IgG anti-fHbp titers (P = 0.001) and 4-fold higher complement-mediated bactericidal titers against a PorA-heterologous strain than the NOMV with the mutant fHbp (P = 0.003). By adsorption, the bactericidal antibodies were shown to be directed at fHbp. In transgenic mice in which human fH bound to the wild-type fHbp but not to the R41S fHbp, the NOMV vaccine with the mutant fHbp elicited 5-fold higher serum IgG anti-fHbp titers (P = 0.002), and 19-fold higher bactericidal titers than the NOMV vaccine with wild-type fHbp (P = 0.001). Thus, in mice that differed only by the presence of human fH, the respective results with the two vaccines were opposite. The enhanced bactericidal activity elicited by the mutant fHbp vaccine in the presence of human fH far outweighed the loss of immunogenicity of the mutant protein in wild-type animals. Engineering fHbp not to bind to its cognate complement inhibitor, therefore, may increase vaccine immunogenicity in humans.     

The effects of nutrient limitation and growth rate in the chemostat on the immunogenicity of Vibrio cholerae

The possibility was examined of using the chemostat to produce cholera vaccine of immunogenicity similar or superior to that of conventional vaccine produced from organisms grown on nutrient agar. The immunogenicity in mice of vaccines prepared from organisms grown under carbon, nitrogen, magnesium and phosphate limitation each at low and high growth rates was inferior to that of conventional vaccine. It was concluded that under the conditions used in this study the chemostat could not be used to produce cholera vaccine of acceptable immunogenicity. The sensitivity of organisms grown under the same conditions in the chemostat to agglutination by specific agglutinating antiserum showed phenotypic variation and under carbon limitation was growth rate related, although the increased sensitivity to agglutination of carbon-limited organisms at high growth rates was not paralleled by increased ability of these organisms to induce agglutinating antibodies.     

Ability of ELISA and a toxin neutralization assay to detect changes in immunogenicity of a recombinant Bacillus anthracis protective antigen vaccine upon storage

We examined the capability of a mouse immunogenicity assay to detect improper storage of a recombinant protective antigen (rPA)-based anthrax vaccine formulated with an aluminum adjuvant, using ELISA and a toxin neutralization assay (TNA) to measure the antibody response to rPA. The vaccine was stored at 4 °C, room temperature (RT) or 37 °C for one, four and eight weeks and used for immunization, along with freshly prepared vaccine. Results showed that, contrary to ELISA, TNA is suitable to detect a loss of immunogenicity of the rPA vaccine following its exposure to RT for a period of eight weeks and to 37 °C for a period as short as 1 week.     

Chitosan Nanoparticle Encapsulated Hemagglutinin-Split Influenza Virus Mucosal Vaccine

Subunit/split influenza vaccines are less reactogenic compared with the whole virus vaccines. However, their immunogenicity is relatively low and thus required proper adjuvant and/or delivery vehicle for immunogenicity enhancement. Influenza vaccines administered intramuscularly induce minimum, if any, mucosal immunity at the respiratory mucosa which is the prime site of the infection. In this study, chitosan (CS) nanoparticles were prepared by ionic cross-linking of the CS with sodium tripolyphosphate (TPP) at the CS/TPP ratio of 1:0.6 using 2 h mixing time. The CS/TPP nanoparticles were used as delivery vehicle of an intranasal influenza vaccine made of hemagglutinin (HA)-split influenza virus product. Innocuousness, immunogenicity, and protective efficacy of the CS/TPP-HA vaccine were tested in influenza mouse model in comparison with the antigen alone vaccine. The CS/TPP-HA nanoparticles had required characteristics including nano-sizes, positive charges, and high antigen encapsulation efficiency. Mice that received two doses of the CS/TPP-HA vaccine intranasally showed no adverse symptoms indicating the vaccine innocuousness. The animals developed higher systemic and mucosal antibody responses than vaccine made of the HA-split influenza virus alone. The CS/TPP-HA vaccine could induce also a cell-mediated immune response shown as high numbers of IFN-γ-secreting cells in spleens while the HA vaccine alone could not. Besides, the CS nanoparticle encapsulated HA-split vaccine reduced markedly the influenza morbidity and also conferred 100% protective rate to the vaccinated mice against lethal influenza virus challenge. Overall results indicated that the CS nanoparticles invented in this study is an effective and safe delivery vehicle/adjuvant for the influenza vaccine.     

A computational approach for identification of epitopes in dengue virus envelope protein: a step towards designing a universal dengue vaccine targeting endemic regions

A major problem in designing vaccine for the dengue virus has been the high antigenic variability in the envelope protein of different virus strains. In this study, a computational approach was adopted to identify a multi-epitope vaccine candidate against dengue virus that may be suitable for large populations in the dengue-endemic regions. Different bioinformatics tools were exploited that helped the identification of a conserved immunological hot-spot in the dengue envelope protein. The tools also rendered the prediction of immunogenicity and population coverage to the proposed 'in silico' vaccine candidate against dengue. A peptide region, spanning 19 amino acids, was identified in the envelope protein which found to be conserved in all four types of dengue viruses. Ten proteasomal cleavage sites were identified within the 19-mer conserved peptide sequence and a total of 8 overlapping putative cytotoxic T cell (CTL) epitopes were identified. The immunogenicity of these epitopes was evaluated in terms of their binding affinities to and dissociation half-time from respective human leukocyte antigen (HLA) molecules. The HLA allele frequencies were studied among populations in the dengue endemic regions and compared with respect to HLA restriction patterns of the overlapping epitopes. The cumulative population coverage for these epitopes as vaccine candidates was high ranging from approximately 80% to 92%. Structural analysis suggested that a 9-mer epitope fitted well into the peptide-binding groove of HLA-A*0201. In conclusion, the 19-mer epitope cluster was shown to have the potential for use as a vaccine candidate against dengue.     

Development of inactivated trivalent vaccine for the teratogenic Aino,Akabane and Chuzan viruses

Aino, Akabane and Chuzan viruses are arthropod-borne (arbo) viruses transmitted by blood-sucking insects like mosquitoes and Culicoides biting midges. These arbovirus infections are mainly associated with abortion, stillbirth and congenital defects in pregnant cattle, sheep and goats, which induces a considerable economic loss in livestock industry. The viruses seem to be widely distributed in Southeast Asia and Australia. As a control strategy, an inactivated trivalent vaccine against Aino, Akabane and Chuzan virus was developed by using binary ethylenimine or formalin as an inactivating agent. The newly developed trivalent vaccine is evaluated for its safety and immunogenicity in animals such as mice, guinea pigs and cattle. The immune responses were significantly detected within 2-weeks after second vaccination without any side effects. Since the field application of experimental vaccine also revealed increased antibodies in inoculated cattle, we demonstrated that these trivalent vaccines could be used as a vaccine to control the arboviral infections in ruminants.     

Differential immunogenicity of a DNA vaccine containing the Streptococcus mutans wall-associated protein A gene versus that containing a truncated derivative antigen A lacking in the hydrophobic carboxyterminal region

Two plasmid DNA constructs were obtained by cloning separately into the eukaryotic expression vector pcDNA3.1/V5-His-TOPO the wall-associated protein A (wapA) gene of Streptococcus mutans GS-5 or its truncated derivative antigen A (agA) gene encoding a known candidate antigen for dental caries vaccine. The immunogenicity of the two constructs, designated pcDNA-wapA and pcDNA-agA, was compared by intranasal immunization of two groups of mice using the cationic DMRIE-C (1,2-dimyristyloxypropyl-3-dimethylhydroxy ethyl ammonium bromide-cholesterol) as an adjuvant. Immunization with pcDNA-wapA or pcDNA- agA resulted in specific salivary IgA and systemic IgG antibodies to the target antigens after two doses given at 3-week intervals. Higher salivary IgA level was observed in the mice immunized with the pcDNA-wapA vaccine compared to those immunized with the pcDNA-agA vaccine. Furthermore, anti-WapA antibody inhibited S. mutans sucrose-dependent adherence suggesting a potential protection against S. mutans colonization of the tooth, while anti-AgA had no significant effect. Indeed, prediction and analysis of protein epitopes showed that WapA contains highly promiscuous MHC-II binding motifs in addition to those found in AgA. Immunodot assay confirmed that WapA bound biotin-labeled dextran, whereas AgA did not. These data indicated that full-length WapA is a better candidate vaccine antigen than the soluble AgA, which is truncated in the hydrophobic membrane and wall-spanning region.     

Preclinical and clinical development of plant-made virus-like particle vaccine against avian H5N1 influenza

The recent swine H1N1 influenza outbreak demonstrated that egg-based vaccine manufacturing has an Achille's heel: its inability to provide a large number of doses quickly. Using a novel manufacturing platform based on transient expression of influenza surface glycoproteins in Nicotiana benthamiana, we have recently demonstrated that a candidate Virus-Like Particle (VLP) vaccine can be generated within 3 weeks of release of sequence information. Herein we report that alum-adjuvanted plant-made VLPs containing the hemagglutinin (HA) protein of H5N1 influenza (A/Indonesia/5/05) can induce cross-reactive antibodies in ferrets. Even low doses of this vaccine prevented pathology and reduced viral loads following heterotypic lethal challenge. We further report on safety and immunogenicity from a Phase I clinical study of the plant-made H5 VLP vaccine in healthy adults 18-60 years of age who received 2 doses 21 days apart of 5, 10 or 20 μg of alum-adjuvanted H5 VLP vaccine or placebo (alum). The vaccine was well tolerated at all doses. Adverse events (AE) were mild-to-moderate and self-limited. Pain at the injection site was the most frequent AE, reported in 70% of vaccinated subjects versus 50% of the placebo recipients. No allergic reactions were reported and the plant-made vaccine did not significantly increase the level of naturally occurring serum antibodies to plant-specific sugar moieties. The immunogenicity of the H5 VLP vaccine was evaluated by Hemagglutination-Inhibition (HI), Single Radial Hemolysis (SRH) and MicroNeutralisation (MN). Results from these three assays were highly correlated and showed similar trends across doses. There was a clear dose-response in all measures of immunogenicity and almost 96% of those in the higher dose groups (2 × 10 or 20 μg) mounted detectable MN responses. Evidence of striking cross-protection in ferrets combined with a good safety profile and promising immunogenicity in humans suggest that plant-based VLP vaccines should be further evaluated for use in pre-pandemic or pandemic situations. TRIAL REGISTRATION: ClinicalTrials.gov NCT00984945.     

Mutual interactions between DTaP-IPV and Haemophilus influenzae type b (Hib)-conjugated vaccines in laboratory animal models.

Potency and/or immunogenicity of three different Haemophilus influenzae type b-conjugated vaccines (Hib) and a DTaP-IPV vaccine alone, and their mutual interactions in DTaP-IPV-Hib combination was tested. In a mouse model, only combination of Act-Hib, in which tetanus toxoid (TT) was as active as non-conjugated TT, significantly increased the immunogenicity and potency of TT component of DTaP-IPV vaccine. Also, only combination of Hib-TITER, in which CRM197 was used as the carrier with DTaP-IPV, increased the potency of diphtheria toxoid (DT) component of DTaP-IPV vaccine significantly. It shows that the additive effect of tested Hib vaccines on immunogenicity and/or potency of TT and DT was mostly due to the existence of TT and CRM197, respectively, as the carrier in the mentioned Hib vaccines. No difference was shown in inoculation of DTaP-IPV and Hib conjugated vaccines in the same syringe or at separate sites. DTaP-IPV had dual effects on anti-Hib capsular polysaccharide (HibCP) responses to Hib vaccines in the mouse model. This duality was probably related to the carrier B-cell epitopes activity of Hib conjugated vaccines. The immunogenicity of TT component of Act-Hib and Amvax Hib-TT in the guinea pig model was shown and combination of mentioned Hib vaccines with DTaP-IPV, remarkably increased anti-TT antibody responses to the TT component of DTaP-IPV vaccine. These confirmed our results in the mouse model. Using two different protocols to evaluate the guinea pig model for induction of anti-HibCP immunity showed that a "long interval" protocol does not have any advantage over the "short interval" protocol. Also, combination of DTaP-IPV with Hib vaccines did not have any noticeable effect on anti-HibCP antibodies in the guinea pig model. Taken together, our observations in laboratory animal models may facilitate a better understanding of the mutual interactions between the different antigen components of a combined vaccine such as DTaP-IPV-Hib vaccine.     

用于疫苗生产的人二倍体细胞研究进展*

人二倍体细胞(human diploid cells, HDCs)作为制备疫苗的重要培养细胞基质备受人们的关注。由于人二倍体细胞与人类基因组相同、无外源因子、对多种病毒易感性、无潜在致瘤性、所制备的人二倍体疫苗(human diploid cell vaccine, HDCV)具有良好的免疫原性和安全性,适合于疫苗的工业化生产。当前,人群中使用的灭活疫苗、减毒疫苗或亚单位疫苗等均依赖于原代细胞、传代细胞和人二倍体细胞,其中用于疫苗制备的人二倍体细胞主要有WI-38、MRC-5、2BS和KMB-17等细胞系。然而,人二倍体细胞为有限性细胞,细胞的来源和培养技术等存在某些缺陷,进而影响其应用。综述了用于疫苗生产的人二倍体细胞及其疫苗制备技术的研究进展,并分析了存在的问题及改进策略。