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Cow milk (CM) allergy is the most prevalent food allergy in young children in the United States and Great Britain. Current diagnostic tests are either unreliable (IgE test and skin prick test) or resource-intensive with risks (food challenges). We sought to determine whether allergen-specific T cells in CM-allergic (CMA) patients have a distinct quality and/or quantity that could potentially be used as a diagnostic marker. Using PBMCs from 147 food-allergic pediatric subjects, we mapped T-cell responses to a set of reactive epitopes in CM that we compiled in a peptide pool. This pool induced cytokine responses in in vitro cultured cells distinguishing subjects with CMA from subjects without CMA. We further used the pool to isolate and characterize antigen-specific CD4 memory T cells using flow cytometry and single-cell RNA/TCR sequencing assays. We detected significant changes in the transcriptional program and clonality of CM antigen-specific (CM+) T cells elicited by the pool in subjects with CMA versus subjects without CMA ex vivo. CM+ T cells from subjects with CMA had increased percentages of FOXP3+ cells over FOXP3− cells. FOXP3+ cells are often equated with regulatory T cells that have suppressive activity, but CM+ FOXP3+ cells from subjects with CMA showed significant expression of interferon-responsive genes and dysregulated chemokine receptor expression compared with subjects without CMA, suggesting that these are not conventional regulatory T cells. The CM+ FOXP3+ cells were also more clonally expanded than the FOXP3− population. We were further able to use surface markers (CD25, CD127, and CCR7) in combination with our peptide pool stimulation to quantify these CM+ FOXP3+ cells by a simple flow-cytometry assay. We show increased percentages of CM+ CD127−CD25+ cells from subjects with CMA in an independent cohort, which could be used for diagnostic purposes. Looking specifically for T H 2 cells normally associated with allergic diseases, we found a small population of clonally expanded CM+ cells that were significantly increased in subjects with CMA and that had high expression of T H 2 cytokines and pathogenic T H 2/T follicular helper markers. Overall, these findings suggest that there are several differences in the phenotypes of CM+ T cells with CM allergy and that the increase in CM+ FOXP3+ cells is a potential diagnostic marker of an allergic state. Such markers have promising applications in monitoring natural disease outgrowth and/or the efficacy of immunotherapy that will need to be validated in future studies. [ABSTRACT FROM AUTHOR]

Copyright of Revista Iberoamericana de Micologia is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

We aimed to investigate immunity against hepatitis B surface antigen (HBsAg) mutants before and after boosters in adolescents who had lost antibodies against HBsAg (anti-HBs) despite neonatal vaccination. We recruited 142 participants from 15 to 21 years old who had received complete vaccination in infancy but became anti-HBs-negative. Cellular immunity to HBsAg and T-cell epitope variants was assessed before and after boosters. Antibody affinity to variants was assessed after boosters. After one dose of booster, 12 out of 140 (8.6%) participants remained anti-HBs-negative. Anti-HBs titres were higher in those participants <17 (geometric mean, 337.9 ± 10.9 vs. 157.4 ± 16.6 mIU/mL, p = 0.012). Before the booster, HBsAg-specific cell proliferation was present in 58 out of 64 (90.6%) participants. The proliferation response rates to T-cell epitopes were 37.8% and 72.6% (p < 0.001) before and after the booster, respectively. The stimulation index improved from 1.25 ± 1.70 to 2.53 ± 2.32 (p < 0.001) for various T-cell epitopes. HBsAg-specific interleukin (IL)-5- and interferon (IFN)-γ-secreting T-cells were enhanced (45 ± 10 and 50 ± 4 to 420 ± 328 and 355 ± 424 spot-forming cells/106 cells, respectively, p < 0.001). IFN-γ-secreting T cells to epitope 16-33 containing R24K and the antibody affinity to sG145R were still significantly lower than to the wild type. In immunized adolescents who lost anti-HBs, around 10% also lost immune memory. Cellular immunity to some T-cell epitope variants improved after the booster. Antibody affinity to sG145R and the IFN-γ-secreting cell response to some epitope 16-33 variants were still impaired even after booster administration. [ABSTRACT FROM AUTHOR]

Plasmodium vivax , an intracellular protozoan, causes malaria which is characterized by fever, anemia, respiratory distress, liver and spleen enlargement. In spite of attempts to design an efficient vaccine, there is not a vaccine against P. vivax. Notable advances have recently achieved in the development of malaria vaccines targeting the surface antigens such as Apical Membrane Antigens (AMA)-1. AMA-1 is a micronemal protein synthesized during the erythrocyte-stage of Plasmodium species and plays a significant role in the invasion process of the parasite into host cells. P. vivax AMA-1 (PvAMA-1) can induce strong cellular and humoral responses, indicating that it can be an ideal candidate of vaccine against malaria. Identification and prediction of proteins characteristics increase our knowledge about them and leads to develop vaccine and diagnostic studies. In the present study several valid bioinformatics tools were applied to analyze the various characteristics of AMA-1 such as physical and chemical properties, secondary and tertiary structures, B- cell and T-cell prediction and other important features in order to introduce potential epitopes for designing a high-efficient vaccine. The results demonstrated that this protein had 57 potential PTM sites and only one transmembrane domain on its sequence. Also, multiple hydrophilic regions and classical high hydrophilic domains were predicted. Secondary structure prediction revealed that the proportions of random coil, alpha-helix and extended strand in the AMA-1 sequence were 53.74%, 27.22%, and 19.4%, respectively. Moreover, 5 disulfide bonds were predicted at positions 14–21aa, 162–192aa, 208–220aa, 247–265aa and 354–363aa. The data obtained from B-cell and T-cell epitopes prediction showed that there were several potential epitopes on AMA-1 that can be proper targets for diagnostic and vaccine studies. The current study presented interesting basic and theoretical information regarding PvAMA-1, being important for further studies in order to design a high-efficiency vaccine against malaria. • Plasmodium vivax is responsible for about a half of all malaria cases outside sub-Saharan Africa. Vivax malaria is characterized by fever, anemia, headache, liver and spleen enlargement. • AMA-1 is a micronemal protein synthesized in Plasmodium species which induces strong cellular and humoral responses. • In the present study, several reliable bioinformatics tools were used to analyze and predict various characteristics of AMA-1 to introduce potential epitopes for designing a high-efficient vaccine. • The results showed that there were several potential B and T cell epitopes in AMA-1, suggesting that it would be an effective vaccine target. • The current study presented interesting basic and theoretical information regarding AMA-1, being important for further in vivo studies in order to design a high-efficiency vaccine against malaria [ABSTRACT FROM AUTHOR]

We have recently reported the submolecular T-cell recognition profile of the C-terminal half (H C , residues 855–1296) of the heavy (H) chain of botulinum neurotoxin type A (BoNT/A) with peripheral blood lymphocytes (PBL) from 25 BoNT-treated cervical dystonia (CD) patients. In the current study, we describe the mapping of the T-cell responses of the patients to the N-terminal half (H N, residues 449–859) of the heavy chain by using 29 synthetic overlapping peptides encompassing the entire H N domain of BoNT/A. The profiles of the T-cell responses to the peptides varied among the patients. Samples from 14 patients treated solely with BoNT/A recognized 1–9 (average 3.7) peptides/sample at Z > 3.0 level. Three peptide regions representing residues 631–649, 659–677 and 743–761 were frequently recognized by 29–64% of the patients. In patients with positive anti-BoNT/A antibody responses the overall positive T cell responses to the H N peptides were significantly increased compared to antibody-negative patients. Influence of treatment parameters on the T-cell recognition of the H N peptides was also observed. The results were compared with those of previously identified H C region. [ABSTRACT FROM AUTHOR]

We determined the T-cell proliferative responses of the peripheral blood lymphocytes (PBL) from 25 botulinum neurotoxin (BoNT)-treated patients to 31 overlapping synthetic peptides encompassing the C-terminal half (residues 855–1296) of BoNT/A heavy chain. Responses of PBL to H C peptides varied among patients. Samples from 14 patients treated solely with BoNT/A recognized 2–13 (average 6.4) peptides/sample at Z > 3.0 level. Six peptide regions representing residues 855–873, 1023–1041, 1051–1069, 1093–1111, 1135–1153 and 1247–1265 were frequently recognized by 36–57% of these PBLs. Influence of treatment parameters on T-cell recognition of the peptides was also investigated. [ABSTRACT FROM AUTHOR]

• Phylogenetic analysis of 4996 Indian SARS-CoV-2 genomes is performed. • Mutation points as SNPs are identified. • Top 10 signature SNPs are selected in each clade. • NSP10 as target is identified and primers and probes are provided for virus detection. • T-cell and B-cell epitopes are predicted. In the worrisome scenarios of various waves of SARS-CoV-2 pandemic, a comprehensive bioinformatics pipeline is essential to analyse the virus genomes in order to understand its evolution, thereby identifying mutations as signature SNPs, conserved regions and subsequently to design epitope based synthetic vaccine. We have thus performed multiple sequence alignment of 4996 Indian SARS-CoV-2 genomes as a case study using MAFFT followed by phylogenetic analysis using Nextstrain to identify virus clades. Furthermore, based on the entropy of each genomic coordinate of the aligned sequences, conserved regions are identified. After refinement of the conserved regions, based on its length, one conserved region is identified for which the primers and probes are reported for virus detection. The refined conserved regions are also used to identify T-cell and B-cell epitopes along with their immunogenic and antigenic scores. Such scores are used for selecting the most immunogenic and antigenic epitopes. By executing this pipeline, 40 unique signature SNPs are identified resulting in 23 non-synonymous signature SNPs which provide 28 amino acid changes in protein. On the other hand, 12 conserved regions are selected based on refinement criteria out of which one is selected as the potential target for virus detection. Additionally, 22 MHC-I and 21 MHC-II restricted T-cell epitopes with 10 unique HLA alleles each and 17 B-cell epitopes are obtained for 12 conserved regions. All the results are validated both quantitatively and qualitatively which show that from genetic variability to synthetic vaccine design, the proposed pipeline can be used effectively to combat SARS-CoV-2. [ABSTRACT FROM AUTHOR]

The search for effective vaccines against chicken coccidiosis remains a challenge because of the complex organisms with multiple life cycle stages of Eimeria . Combination of T-cell epitopes from different stages of Eimeria life cycle could be an optimal strategy to overcome the antigen complexity of the parasite. In this study, 4 fragments with concentrated T-cell epitopes from the sporozoite antigen SO7 and the merozoite antigen MZ5-7 of Eimeria tenella were cloned into eukaryotic expression vector pVAX1 in different forms, with or without chicken cytokines IL-2 or IFN-γ genes as genetic adjuvants, to construct multistage, multi-epitope DNA vaccines against Eimeria tenella . Transcription and expression of the multi-epitope DNA vaccines in vivo were detected by reverse transcription-PCR (RT-PCR) and Western blot. On the basis of survival rate, lesion score, body weight gain, oocyst decrease ratio and the anti-coccidial index (ACI), Animal experiments were carried out to evaluate the protective efficacy against Eimeria tenella. Results showed the constructed DNA vaccines were transcribed and translated successfully in vivo . Animal experiment showed that the multi-epitopes DNA vaccines were more effective to stimulate immune response than single fragment. Compared with the DNA vaccines composed with less T-cell epitopes, DNA vaccine pVAX1-m1-m2-s1-s2 containing 4 fragments with concentrated T-epitopes provided the highest ACI of 180.39. DNA vaccines composed of antigens from two developmental stages were more effective than the single-stage ones. Especially DNA vaccine pVAX1-m1-m2-s1-s2 provided the most effective protection with the ACI of 180.39. Furthermore, cytokines IL-2 or IFN-γ could improve the efficacy of the multi-epitope DNA vaccines significantly. Overall, pVAX1-m1-m2-s1-s2-IFN-γ provided the most effective protection with the ACI of 189.92. The multi-epitope DNA vaccines revealed in this study provide new candidates for Eimeria vaccine development. [ABSTRACT FROM AUTHOR]

Abstract: Immunotherapies with T-cell epitope peptides have shown a promising impact over allergic diseases as a potential therapeutic tool in in vitro and in vivo conditions. It is recognized as an effective treatment with long lasting clinical effects and subsequent reduction of the allergic inflammatory reactions. In this review, we have summarized the role of peptide based immunotherapy and emphasis has been given to the recent advancement in pollen, cat, hymenoptera venom, and food allergy. [Copyright &y& Elsevier]

Highlights: [•] An effective approach has been developed for T-cell epitopes prediction. [•] A combined feature has been provided to show significant improvement in accuracy. [•] Random forest provides some useful tools to select informative features and make classification simultaneously. [•] A freely available web server of for predicting peptide immunogenicity is established. [Copyright &y& Elsevier]

Abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is a significant swine pathogen which exhibits considerable sequence diversity. In an attempt to identify highly conserved T-cell epitopes contained in proteins of this virus, we examined heptadecamer peptides spanning the sequence of the PRRSV nonstructural proteins (NSPs) 9 and 10, both of which are highly conserved, for their ability to elicit a recall proliferative and interferon-gamma response in peripheral blood mononuclear cells obtained from pigs immunized against the type-II PRRSV strain FL-12. These studies led to the identification of four peptides, two from each NSP9 and NSP10 that appear to contain T-cell epitopes. Comparison of the amino acid sequence of these four peptide sequences to the analogous sequences from a diverse sample of type-II PRRSV strains indicated that these sequences are highly conserved and thus contain highly conserved T-cell epitopes. The identified epitopes may be important in the formulation of immunogens to provide broad cross-protection against diverse PRRSV strains. [Copyright &y& Elsevier]

Abstract: Primary approach to prevent cervical cancer includes the development of human papillomavirus (HPV) vaccines. Currently available HPV vaccines (Gardasil and Cervarix) predominantly consider HPV16 and HPV18 strains. However, due to ignorance of the other high-risk strains aside from HPV16 and HPV18 during vaccine development, the critical need is to synthesize a vaccine with possible protection against all the high-risk HPV types. One feasible approach is to design a vaccine containing conserved immunogenic peptides that represent the genotypic diversity of all the current and future high-risk HPV types. While the epitopes derived from sequentially conserved regions may undergo mutations, it is worthwhile to explore the structurally conserved regions as a new dimension for epitope prediction. In the present study, 81 structurally conserved peptides were predicted to have immune relevance as T-cell epitopes of all the reported high-risk HPV proteins studied. A small dataset of three epitopes was also recognized as potential vaccine candidates generating both CD8+ and CD4+ responses. [Copyright &y& Elsevier]

Abstract: The current poxvirus vaccine is associated with rare, but serious adverse events. Therefore, we investigated a non-replicating approach to vaccine design. Peptides encoding potential HLA-binding motifs were derived from the orthopoxvirus genes, D8L, A27L, and C12L (the IL-18-binding protein [vIL18BP105]), all of which are preserved among poxviruses that infect humans, and which may be a target of host immunity. The peptides were tested with poxvirus-vaccinated human PBMC and serum for eliciting memory responses, as well as with splenocytes and serum from peptide-immunized, human HLA-DR04 transgenic (HLA tg) mice. vIL18BP105 induced 5-fold proliferation of vaccinated-donor PBMC over non-vaccinated (P <0.001), including IL-2-producing CD8+ cells. Serum IgG recognizing vIL18BP105 was detected (P <0.002 vs non-vaccinated) by ELISA. Viral peptides were conjugated to the HLA-targeting mAb, L243, for immunization of HLA tg mice. Splenocytes from vIL18BP105-L243-immunized mice proliferated upon exposure to vIL18BP105 (P <0.001). Proliferating splenocytes were interferon-γ-producing CD4+CD45RAneg. vIL18BP105-L243-immunized mice generated IgG more rapidly than free-peptide-immunized mice. Peptide-specific antibody was also detected when different L243-peptide conjugates were combined. vIL18BP, by eliciting human memory responses, is a viable antigen for inclusion in a virus-free vaccine. The immunogenicity of peptides was boosted by conjugation to L243, whether administered alone or combined. [Copyright &y& Elsevier]

Abstract: Herpes simplex virus (HSV) infection is a major health concern worldwide. Evidence obtained from animals and humans indicates that B- and T-cell responses contribute to protective immunity against herpes virus infection. Glycoprotein B is a transmembrane envelope component of HSV-1 and HSV-2, which plays an important role in virion morphogenesis and penetration into host cells, and can induce neutralizing antibodies and protective T-cell response when it is used to immunize humans and animals. However, little is known about gB epitopes that are involved in B- and T-cell activities in vitro and in vivo. Thus, the HSV-2 gB sequence was screened using B- and T-cell epitope prediction systems, and the B-cell regions and the HLA-A*0201-restricted epitopes were identified. These B-cell epitopes elicited high IgG antibody titers in Balb/C mice, with a predominantly IgG1 subclass distribution, which indicated a Th2 bias. Specific IgGs induced by these two epitopes were evaluated as the neutralizing antibodies for virus neutralization. The predicted T-cell epitopes stabilized the HLA-A*0201 molecules on T2 cells, and stimulate interferon-γ-secreting and cytotoxic CD8+ T cells. Immunization with the predicted peptides reduced virus shedding and protected against lethal viral challenge in mice. The functional epitopes described herein, both B- and T-cell epitopes, are potentially implicated in vaccine development. [Copyright &y& Elsevier]

Abstract: This review will discuss the current state of the human HIV-1 vaccine trials including the safety consideration of vaccine composition and difficulties in determining and defining protective immunity and epitopes to HIV-1. Vaccines in animal models of lentivirus infection are compared. In particular, the findings from the prototype FIV vaccine and the HIV-1 protein immunizations studies in cats are discussed, as well as the resulting research regarding a potential HIV-1 vaccine design based on evolutionarily conserved T-cell epitopes. [Copyright &y& Elsevier]

Abstract: The low-molecular-mass secretory proteins of Mycobacterium tuberculosis have been shown to be major T-cell antigens during infection with the pathogenic bacterium. In this study, we determined murine T-cell epitopes on three low-molecular-mass proteins, CFP11 (Rv2433c), CFP17 (Rv1827), and TB18.5 (Rv0164) using DNA immunization of inbred mice. We analyzed interferon-γ production from immune splenocytes in response to overlapping peptides covering these proteins. We identified two CD8+ T-cell epitopes on CFP11 and CFP17, one in BALB/c mice and the other in C57BL/6 mice, respectively. On TB18.5, we identified a CD8+ T-cell epitope in BALB/c mice and a CD4+ T-cell epitope in C57BL/6 mice. With the aid of computer algorithms, we could identify the minimal CD8+ T-cell epitopes. These T-cell epitopes are feasible for analysis of the role of antigen-specific T cells during M. tuberculosis infection. [Copyright &y& Elsevier]

Abstract: Identification of CTL epitopes correlated to immune protection is important for the development of vaccines that enhance T-cell mediated immune responses. The correlation of positively selected amino acids (PS) of HIV-1 with host HLA alleles can identify regions containing potential T-cell epitopes. However, the specific epitopes have to be identified and characterized using overlapping peptides through T-cell functional assays. In this study we used a new approach to identify and characterize potential epitopes in the gag region containing PS mutations that significantly correlated with HLA-A*0301. The iTopia Epitope Discovery System was used to rapidly screen a panel of peptides overlapping the regions containing PS mutations and the peptides identified were assessed for relative affinity and complex stability. The potential epitopes were then validated by interferon gamma (IFN-γ) ELISpot assays with patient PBMCs. Using this approach we identified/confirmed the predicted HLA-A*0301 epitopes in two regions of gag containing PS mutations V7I and K403R, one previously reported and the other novel. Five of the seven peptides that bound to A*0301 contained the K403R mutation and corresponded to the documented LARNCRAPRK-A3 supertype epitope. Two epitope variants, RASVLSGGK and RASILSGGK containing the V7I mutation, were identified using the iTopia Epitope Discovery System, however only the consensus variant (RAK9C) was confirmed using the ELISpot assay and it represents a novel A*0301 epitope. [Copyright &y& Elsevier]

Abstract: T-cell epitopes of porcine reproductive and respiratory syndrome virus (PRRSV) glycoproteins 4 (GP4), 5 (GP5) and nucleocapsid (N) were predicted using bioinformatics and later tested by IFN-γ ELISPOT in pigs immunized with either a modified live vaccine (MLV) or DNA (open reading frames 4, 5 or 7). For MLV-vaccinated pigs, immunodominant epitopes were found in N but T-epitopes were also found in GP4 and GP5. For DNA-immunized pigs, some peptides were differently recognized. Using a large set of PRRSV sequences it was shown that N contains a conserved epitope and that for GP5, the genotype-I counterparts of previously reported epitopes of genotype-II strains were also immunogenic. [Copyright &y& Elsevier]

Copyright of Revue Francaise d'Allergologie is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract: A set of new amino acid descriptors, namely factor analysis scales of generalized amino acid information (FASGAI) involving hydrophobicity, alpha and turn propensities, bulky properties, compositional characteristics, local flexibility and electronic properties, was proposed to resolve the representation of peptide structures. FASGAI vectors were then used to represent the structures of 152 HLA-A∗0201 restrictive T-cell epitopes with 9 amino acid residues. The features that are closely related to binding affinities were selected by genetic arithmetic, and the model based on partial least squares was developed to predict binding affinities. The model revealed promising predictive power, giving relatively high predictions for training and test samples. Further, the PreMHCbinding program at significantly lower computational complexity was exploited to predict MHC class I binding peptides. Quantitative structure–affinity relationship analyses demonstrated the bulky properties and hydrophobicity of the 3rd residue, bulky properties of the 2nd residue, hydrophobicity of the 9th residue that provided high positive contribution to the binding affinities, and that the hydrophobicity of the 4th residue and local flexibility of the 3rd residue were negative to binding affinities. The results showed that FASGAI vectors can be further utilized to represent the structures of other functional peptides; moreover, it has thus showed us further direction into the potential applications on relationship between structures and functions of proteins. [Copyright &y& Elsevier]

Abstract: Exploring the intricacies of CD8+ T-cell epitope recognition using emerging technologies to combine assessment of affinity, phenotype and resulting polyfunctional efficacy advances our understanding of HIV-1 immunopathogenesis and disease progression. Complexities within T-cell antigen recognition, such as epitope:MHC binding, stability and affinity, appear to influence the distinction between protective and ineffective anti-HIV-1 immune responses, which are thought to govern rate of disease progression. This study utilises the novel ProImmune REVEAL and ProVE® technology of rapid peptide synthesis, binding and affinity assays, and pentamer synthesis in conjunction with flow cytometry and simultaneous assessment of multiple CD8+ T-cell effector functions in response to HLA-B⁎3501-restricted HIV-1 Gag peptides, to discover new T-cell epitopes. The predicted HLA-B⁎3501-restricted peptides, HPVHAGPIA and YPLTSLRSL, and relevant pentamers were used in parallel to validate T-cell epitopes on clinical HIV-1+ samples, confirming correlation between the expected superior immunogenicity of newly discovered epitopes and the ex vivo T-cell response. Such a platform should be employed in prophylactic and therapeutic vaccine settings. [Copyright &y& Elsevier]

Abstract: In order to reconstruct the system for identification of short antigenic peptides, the chicken BF2 gene of Chinese Sanhuang (SH) chicken line was linked to the β 2 m gene via (G4S)3, a linker encoding a 15-amino acid glycine-rich peptide, by splicing overlap extension PCR (SOE-PCR). The MBP–BF2–(G4S)3–β2m fusion protein was expressed and purified in a pMAL-p2X/E. coli TB1 system. The purified MBP–BF2–(G4S)3–β2m protein was cleaved by Factor Xa protease, and further purified by DEAE–Sepharose chromatography. The conformation of the BF2–(G4S)3–β2m protein was determined by circular dichroism (CD). In addition, the refolded BF2–(G4S)3–β2m protein was used to bind three predicted nonameric peptides derived from the hemagglutinins of the avian influenza virus (AIV) H5N1 and H9N2 subtypes. The BF2–(G4S)3–β2m-associated peptides were detected by mass spectrometry. The molecular weights and amino acid sequences of the peptides were confirmed by primary and tandem mass spectrometry analysis, respectively. The results indicate that the secondary structures and predicted three-dimensional crystal structure of BF2–(G4S)3–β2m are similar to those of the monomers of chicken BF2 and β2m. The BF2–(G4S)3–β2m protein could bind two of the three predicted nonamer peptides derived from AIV hemagglutinin. The experimental system demonstrated that the reconstructed BF2–(G4S)3–β2m protein complex can be used to identify nonamer peptides, including T-cell epitopes in chicken. [Copyright &y& Elsevier]

In this paper, we propose a new encoding technique that combines the different physicochemical properties of amino acids together with Needleman–Wunsch algorithm. The algorithm was tested in the recognition of T-cell epitopes. A series of SVM classifiers, where each SVM is trained using a different physicochemical property, combined with the “max rule” enables us to obtain an improvement over the state-of-the-art approaches. [Copyright &y& Elsevier]

Abstract: Ninty-six pentadecapeptides spanning glycoprotein 5 (GP5) of porcine reproductive and respiratory virus (PRRSV) were screened for their ability to elicit a recall interferon-γ response from peripheral blood mononuclear cells isolated from 22 pigs infected with up to two genetically divergent PRRSV strains. Two distinct regions (amino acid residues 117–131, LAALICFVIRLAKNC, and 149–163, KGRLYRWRSPVII/VEK) appeared to contain immunodominant T-cell epitopes based on their ability to stimulate above average numbers of interferon-γ secreting cells as compared to other GP5 peptides. A survey of PRRSV isolates indicated that these two sites are relatively conserved with at most a two amino acid variation and thus should be considered for incorporation into a multi-valent vaccine against PRRS. [Copyright &y& Elsevier]

Abstract: Identification of CD4+ T-cell epitopes is a critical step in studying and modulating the immune responses to tumors, infectious agents, and autoantigens. Here we report a facile, accurate, and high-throughput method for CD4+ T-cell epitope identification using yeast displaying pathogen-derived peptide library. A library of DNA fragments that encode all the possible peptides with 10–20 amino acids from the antigens (single antigenic proteins or pathogenic organisms) are fused to the gene encoding the restriction single-chain MHC class II molecule in a yeast display vector. The resultant library of recombinant yeast cells are analyzed by FACS to identify those containing peptides with high affinity towards the restriction MHC molecule, which are subsequently screened for their ability to induce antigen-specific T-cell activation. DNA sequence analysis of selected positive clones results in direct identification of the antigenic peptides. We show that this method can be used to rapidly pinpoint the HA306–322 epitope from the haemagglutinin protein and the entire influenza virus X31/A/Aichi/68 genome, respectively. [Copyright &y& Elsevier]

Abstract: Introduction: : Cry-consensus peptide is a linearly linked peptide of T-cell epitopes for the management of Japanese cedar (JC) pollinosis and is expected to become a new drug for immunotherapy. However, the mechanism of T-cell epitopes in allergic diseases is not well understood, and thus, a simple in vitro procedure for evaluation of its biological activity is desired. Methods: : Peripheral blood mononuclear cells (PBMC) were isolated from 27 JC pollinosis patients and 10 healthy subjects, and cultured in vitro for 4 days in the presence of Cry-consensus peptide and 3H-thymidine. The relationship between growth stimulation (stimulation index; SI) and antigen-specific IgE levels in serum was also investigated in JC pollinosis patients. Moreover, to confirm the importance of the primary sequence in Cry-consensus peptide, heat-treated Cry-consensus peptide and a mixture of the amino acids of which Cry-consensus peptide is composed, and their 3H-thymidine uptake was compared with Cry-consensus peptide. Finally, whether Cry-consensus peptide stimulates PBMCs from healthy subjects was investigated. Results: : The mean SI of JC patients showed a good correlation with Cry-consensus peptide concentration in the culture medium; however, the SI was independent of the anti-Cry j 1 IgE level. Heat-denatured Cry-consensus peptide retained a PBMC proliferation stimulatory effect comparable to the original Cry-consensus peptide, while the mixture of amino acids constituting Cry-consensus peptide did not stimulate PBMC proliferation. PBMCs from healthy subjects did not respond to Cry-consensus peptide at all. Discussion: : These data indicate that the PBMC response of patients suffering from JC pollinosis to Cry-consensus peptide is specific for the sequence of T cell epitopes thereof and may be useful for the evaluation of the efficacy of Cry-consensus peptide in vivo. [Copyright &y& Elsevier]

Abstract: T-lymphocyte (T-cell) is a very important component in human immune system. It possesses a receptor (TCR) that is specific for the foreign epitopes which are in a form of short peptides bound to the major histocompatibility complex (MHC). When T-cell receives the message about the peptides bound to MHC, it makes the immune system active and results in the disposal of the immunogen. The antigenic determinants recognized and bound by the T-cell receptor is known as T-cell epitope. The accurate prediction of T-cell epitopes is crucial for vaccine development and clinical immunology. For the first time we developed new models using least squares support vector machine (LSSVM) and amino acid properties for T-cell epitopes prediction. A dataset including 203 short peptides (167 non-epitopes and 36 epitopes) was used as the input dataset and it was randomly divided into a training set and a test set. The models based on LSSVM and amino acid properties were evaluated using leave-one-out cross-validation method and the predictive ability of the test set, and obtained the results of 0.9875 and 0.9734 under the ROC curves, respectively. This result is more satisfactory than that were reported before. Especially, the accuracy of true positive gets a marked enhancement. [Copyright &y& Elsevier]

The allergic response in human beings is engineered by CD4+ T lymphocytes, which secrete TH2 cytokines in response to activation by allergen-derived peptides. Although TH2 cells have been well characterized, defining the properties of allergen-specific T cells has proved challenging in human beings because of their low frequency within the T-cell repertoire. However, recent studies have provided insight into the molecular signature of long-lived human memory TH2 cells, which are allergen-specific. T-cell responses directed against allergens develop in early life and are heavily influenced by the type and dose of allergen, and possibly coexposure to microbial products. These responses are susceptible to suppression by regulatory T cells. This article highlights recent advances in the characterization of allergen-specific memory TH2 cells and discusses the heterogeneous nature of regulatory T cells and possible mechanisms of action. The relevance of T-cell epitope mapping studies to understanding the unique nature of T-cell responses to different allergens, as well as to peptide vaccine development, is reviewed. Experimental techniques and approaches for analyzing allergen-specific T cells and identifying novel T-cell epitopes are described that may lead to new T-cell–based therapies. [Copyright &y& Elsevier]

Abstract: To identify foot-and-mouth disease virus (FMDV) specific T-cell epitopes within the non-structural protein 3D in swine, pentadecapeptides were tested in proliferation and Interferon-γ ELISPOT assays using lymphocytes from two strains of inbred miniature pigs (c/c and d/d haplotype) experimentally infected with FMDV. Lymphocytes of c/c pigs recognized peptides from three different regions in 3D, d/d lymphocytes recognized peptides from two regions, one of them being adjacent to an epitope of c/c pigs and comprising amino acid residues 346–370. Analyses of the response of d/d lymphocytes against peptides representing the structural protein 1A revealed another novel T-cell epitope. Investigation of the phenotype of responding lymphocytes showed a response of CD4+CD8+MHC-class-II+ cells, identifying them as activated T-helper cells. This is the first report on FMDV specific T-cell epitopes recognized by swine leukocyte antigen (SLA) inbred swine and provides information useful for the design of novel vaccines against FMDV. [Copyright &y& Elsevier]

Abstract: The RhD protein is expressed only on human red blood cells (RBC), and is one of the most immunogenic of the blood groups. It is of clinical importance since the alloantibody (anti-D) can hemolyse D positive RBC after blood transfusion, or cause hemolytic disease of the newborn. The immunogenicity of D is better understood with the knowledge of the genetic basis of the protein(s) involved, the molecular orientation in the RBC membrane, and the nature of the cellular immune response to proteins. The adaptive humoral response consists of antigen presenting cells, T-cells and B-cells, which interact cooperatively to result in antibody against the antigen in question. The anti-D that B-cells produce is targeted against surface membrane determinants (B-cell epitopes) and are conformational i.e. non-contiguous amino acids. The antigen specific T-cells recognize short linear peptides in the context of MHC class II, and these T-cell epitopes can reside anywhere in the protein. Since the RhD protein in D-positive individuals differs by some 35 amino acids from the RhCcEe protein in D-negative individuals, the opportunity for generating immunogenic T-cell epitopes is much greater than that for alleles characterized by a single amino acid difference e.g. E and e. Multiple conformational B-cell epitopes are also created by the presence of several D-specific amino acids in extracellular loops on the red cells surface, which may stimulate several B-cell clones and develop a strong polyclonal antibody response. With greater understanding comes the possibility of manipulating the immune response to D in clinical situations. [Copyright &y& Elsevier]

Abstract: As an in vivo model for studying human MHC (HLA) class I-restricted CTL responses to viral infection, we established a series of HLA Tg mice expressing HLA-A2, -B7 or -B27 human/mouse hybrid genes on a background deficient for H2 class I (Tg HLAhyb/H2 class I DKO). To determine whether CTL recognition of influenza A (flu) infection in Tg HLA-A2hyb/H2 DKO mice is similar to HLA-A2+ humans, we compared the HLA-A2-restricted Tg mouse and human CD8+ T-cell responses to an immunodominant flu epitope (wild-type [WT] M1 58–66), as well as a variant of this peptide (var. M1 58–66). Similar to HLA-A2+ humans, our results show WT M1 58–66 is likely the dominant CTL epitope recognized in infected Tg HLA-A2hyb/H2 DKO mice. Var. M1 58–66 was also recognized by WT peptide-reactive T cells from both HLA-A2+ humans and Tg mice, although slightly less efficiently than WT M1 58–66 in both cases. Reduced variant recognition was shown to be associated with reduced peptide/A2 binding, as well as a more limited repertoire of utilized TCR Vβ chains. The similar pattern of recognition and cross reaction observed here for the WT and variant M1 58–66 epitopes with HLA-A2 by human and Tg HLA mouse CTLs indicates that A2-dependent events of Ag processing, presentation and recognition are well-conserved between species. These findings demonstrate that this Tg HLA-A2/H2 DKO model will aid identification and development of epitopes as vaccines for numerous viral and tumor antigens for the HLA-A2 supertype. [Copyright &y& Elsevier]

Abstract: Three-dimensional models of the major vicilin allergens from peanut (Ara h 1), lentil (Len c 1) and pea (Pis s 1), were built by homology-based modelling from the X-ray coordinates of the structurally closely related soybean β-conglycinin. All the allergen monomers exhibit the typical cupin motif made of two modules related by a pseudo-dyad axis. Each module consists of a β-barrel core domain associated to a loop domain which mainly contains α-helices. The three cupin motifs are assumed to be arranged in a homotrimeric structure similar to that observed in β-conglycinin, phaseolin or canavalin. Most of the sequential B-cell epitopes characterized on the C-terminus of the Ara h 1 allergen are well conserved in both Len c 1 and Pis s 1 allergens. They occupy very comparable areas on the molecular surface of the allergens and exhibit a similar three-dimensional conformation. This antigenic community readily accounts for the IgE-binding cross-reactivity commonly observed between the vicilin allergens from edible legume seeds. The clinical implication of this cross-reactivity is addressed for a definite diagnosis of legume seed allergy. [Copyright &y& Elsevier]

Japanese cedar (Cryptomeria japonica, CJ) pollen has been known to cause atopic dermatitis in dogs in Japan. However, since the mechanism of the CJ antigen recognition is not well understood in dogs, it is difficult to develop effective immunotherapy for atopic dermatitis caused by sensitization to CJ pollen. In order to aim at development of a peptide immunotherapy, we tried to identify T-cell epitopes of a major allergen of CJ pollen, Cry j 1, in dogs sensitive to CJ pollen allergen. Peripheral blood mononuclear cells (PBMCs) obtained from 22 dogs experimentally sensitized to CJ pollen allergen and 5 atopic dogs sensitive to CJ pollen allergen were used for mapping of T-cell epitopes of Cry j 1 using 35 kinds of synthesized overlapping peptides of Cry j 1. Reactive peptides were identified based on the results of blastogenic responses of PBMCs against the peptides when the stimulation indices were beyond 2.0. Three reactive peptides were identical in a relatively high population of experimental dogs, which were Nos. 8 (p71–90) (41%), 10 (p91–110) (50%), and 11 (p101–120) (41%). It was considered that these synthesized peptides should contain T-cell epitopes of Cry j 1 in the dogs. However, there were no reactive peptides identical among the five atopic dogs spontaneously sensitive to CJ pollen. The population of dogs experimentally sensitized to CJ pollen antigen will be used in order to investigate effects of a peptide immunotherapy using the reactive peptides. The results in atopic dogs sensitive to CJ pollen antigen will also provide useful information on necessity to develop a tailor-made immunotherapy using reactive peptides in each dog. [Copyright &y& Elsevier]

The surge of SARS-CoV-2 has created a wave of pandemic around the globe due to its high transmission rate. To contain this virus, researchers are working around the clock for a solution in the form of vaccine. Due to the impact of this pandemic, the economy and healthcare have immensely suffered around the globe. Thus, an efficient vaccine design is the need of the hour. Moreover, to have a generalised vaccine for heterogeneous human population, the virus genomes from different countries should be considered. Thus, in this work, we have performed genome-wide analysis of 10,664 SARS-CoV-2 genomes of 73 countries around the globe in order to identify the potential conserved regions for the development of peptide based synthetic vaccine viz. epitopes with high immunogenic and antigenic scores. In this regard, multiple sequence alignment technique viz. Clustal Omega is used to align the 10,664 SARS-CoV-2 virus genomes. Thereafter, entropy is computed for each genomic coordinate of the aligned genomes. The entropy values are then used to find the conserved regions. These conserved regions are refined based on the criteria that their lengths should be greater than or equal to 60 nt and their corresponding protein sequences are without any stop codons. Furthermore, Nucleotide BLAST is used to verify the specificity of the conserved regions. As a result, we have obtained 17 conserved regions that belong to NSP3, NSP4, NSP6, NSP8, RdRp, Helicase, endoRNAse, 2'-O-RMT, Spike glycoprotein, ORF3a protein, Membrane glycoprotein and Nucleocapsid protein. Finally, these conserved regions are used to identify the T-cell and B-cell epitopes with their corresponding immunogenic and antigenic scores. Based on these scores, the most immunogenic and antigenic epitopes are then selected for each of these 17 conserved regions. Hence, we have obtained 30 MHC-I and 24 MHC-II restricted T-cell epitopes with 14 and 13 unique HLA alleles and 21 B-cell epitopes for the 17 conserved regions. Moreover, for validating the relevance of these epitopes, the binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles. Also, the physico-chemical properties of the epitopes are reported along with Ramchandran plots and Z -Scores and the population coverage is shown as well. Overall, the analysis shows that the identified epitopes can be considered as potential candidates for vaccine design. • Genome-wide analysis of 10,664 SARS-CoV-2 genomes of 73 countries. • Identification of 17 potential conserved regions. • Identification of 30, 24 and 21 best immunogenic and antigenic MHC-I and MHC-II T-cell and B-cell epitopes. • Physico-chemical properties of the epitopes are studied. • Docking with Ramachandran Plot and Z-score are performed. [ABSTRACT FROM AUTHOR]

• Genome-wide analysis of 566 Indian SARS-CoV-2 genomes. • Finding potential 23 consensus conserved regions. • 34, 37 and 29 best immunogenic and antigenic MHC-I, MHC-II T-cell and B-cell epitopes. • Physico-chemical properties of the epitopes are studied. • Docking with Ramachandran Plot and Z-score are performed. SARS-CoV-2 has a high transmission rate and shows frequent mutations, thus making vaccine development an arduous task. However, researchers around the globe are working hard to find a solution e.g. synthetic vaccine. Here, we have performed genome-wide analysis of 566 Indian SARS-CoV-2 genomes to extract the potential conserved regions for identifying peptide based synthetic vaccines, viz. epitopes with high immunogenicity and antigenicity. In this regard, different multiple sequence alignment techniques are used to align the SARS-CoV-2 genomes separately. Subsequently, consensus conserved regions are identified after finding the conserved regions from each aligned result of alignment techniques. Further, the consensus conserved regions are refined considering that their lengths are greater than or equal to 60nt and their corresponding proteins are devoid of any stop codons. Subsequently, their specificity as query coverage are verified using Nucleotide BLAST. Finally, with these consensus conserved regions, T-cell and B-cell epitopes are identified based on their immunogenic and antigenic scores which are then used to rank the conserved regions. As a result, we have ranked 23 consensus conserved regions that are associated with different proteins. This ranking also resulted in 34 MHC-I and 37 MHC-II restricted T-cell epitopes with 16 and 19 unique HLA alleles and 29 B-cell epitopes. After ranking, the consensus conserved region from NSP3 gene is obtained that is highly immunogenic and antigenic. In order to judge the relevance of the identified epitopes, the physico-chemical properties and binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles. [ABSTRACT FROM AUTHOR]

• B-cell epitopes is the antigen portion binding to the immunoglobulin or antibody. • T-Cell epitope play a crucial role in eliciting vigorous protective immune response. • Antigenicity refers to the capacity of virus to bind to specific antibody molecule. The beginning of 2020 was marked as the emergence of a COVID-19 outbreak caused by a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, there is no vaccine or approved treatment for this infectious virus so the invention of an efficient vaccine is certainly a high priority. Some studies have employed several techniques to facilitate the combination of the immunoinformatics approach and comparative genomic approach in order to determine the potential peptides for designing the T-cell epitope-based peptide vaccine using the 2019-nCoV envelope protein as a target. Via screening the bioimmunoinformatic SARS-CoV2 derived B-cell and T-cell epitopes within the basic immunogenic of SARS-CoV2 proteins, we presented a set of inferred B-cell and T-cell epitopes from the spike (S) and nucleocapsid (N) proteins with high antigenicity and without allergenic property or toxic effects. Our findings provide a screened set of epitopes that can be introduced as potential targets for developing peptide vaccines against the SARS-CoV-2 virus. [ABSTRACT FROM AUTHOR]

Background: Although antigen processing and presentation of allergens to CD4+T lymphocytes are key events in the pathophysiology of allergic disorders, they still remain poorly understood. Objective: To investigate allergen processing and presentation by dendritic cells using the major birch pollen allergen Bet v 1 as a model. Methods: Endolysosomal extracts of dendritic cells derived from patients with birch pollen allergy were used to digest Bet v 1. Dendritic cells were pulsed with Bet v 1, and peptides were eluted from MHC class II molecules. Peptides obtained by either approach were sequenced by tandem mass spectrometry. Bet v 1–specific T-cell cultures were stimulated with HLA-DR–eluted Bet v 1–derived peptides. Bet v 1–specific T-cell lines were generated from each patient and analyzed for epitope recognition. Results: A high proportion of Bet v 1 remained intact for a long period of endolysosomal degradation. The peptides that appeared early in the degradation process contained frequently recognized T-cell epitopes. Bet v 1–derived peptides eluted from MHC class II molecules corresponded to those generated by endolysosomal degradation, matched known T-cell epitopes, and showed T cell–activating capacity. The Bet v 1–specific T-cell line of each individual harbored T cells reactive with peptides located within the MHC class II–eluted Bet v 1–derived sequences demonstrating their occurrence in vivo. Conclusion: We report for the first time how epitopes of allergens are generated and selected for presentation to T lymphocytes. The limited susceptibility of Bet v 1 to endolysosomal processing might contribute to its high allergenic potential. [Copyright &y& Elsevier]