Identification and functionalization of thyrotropin receptor antibodies with different antigenic epitopes.

One of the sensitive markers for autoimmune thyroid disease (AITD) clinical identification is thyroid-stimulating hormone receptor antibodies (TRAbs). To quickly distinguish TRAb with distinct antigenic epitopes, a straightforward and uncomplicated technique has not yet been created. The objective of this study is to search for molecular diagnostic targets for different types of AITD {Graves' disease (GD), Graves' orbitopathy (GO), GD with third-degree goiter [GD(3)], hypothyroidism combined with positive TRAb [HT(TRAb+)]} as molecular diagnostic targets. Following action on thyroid cells, differential genes (DEGs) generated by TRAb with distinct antigenic epitopes were detected and identified by RNA sequencing (RNA-Seq), bioinformatics analysis, and quantitative reverse transcription-polymerase chain reaction (RT-qPCR) in the serum of patients with AITD. Using the 5-ethynyl-2'-deoxyuridine (EdU) assay, the effect of coculturing thyroid cells with different antigenic TRAb epitopes on the cells' capacity to proliferate was investigated. Bioinformatics analysis and RT-qPCR validation identified one GD key gene alpha 2-HS glycoprotein (AHSG), two GO key genes [adrenoceptor alpha 1D (ADRA1D) and H2B clustered histone 18 (H2BC18)], two GD(3) key genes [suppressor of cytokine signaling 1 (SOCS1) and cytochrome b-245 beta (CYBB)], and one HT(TRAb+) key gene (MASP2). Correlation analysis and ROC curves showed that the abovementioned genes could be used as molecular diagnostic targets for different types of AITD. Finally, EdU results showed that TRAb inhibited thyroid cell proliferation in the HT(TRAb+) group compared with the normal control group, whereas the remaining three groups promoted thyroid cell proliferation, with a statistically significant difference (P < 0.05). We identified six key genes for different types of AITD, which have diagnostic value for different types of AITD. Meanwhile, we found that TRAbs with different antigenic epitopes in AITD have different biological functions.NEW & NOTEWORTHY We identified six molecular targets of different types of AITD [GD, GO, GD(3), and HT(TRAb+)], which have diagnostic value for different types of AITD. Meanwhile, we found that TRAb with different antigenic epitopes extracted from the sera of patients with AITD had different biological functions, which also provided a new idea for further research on the mechanism of action of TRAb with different antigenic epitopes in AITD.

Identification of allergenic epitopes destroyed by two processing technologies of glycinin A2 from soybean.

BACKGROUND: Glycinin is one of the most highly allergenic proteins in soybeans, and G2 is one of the five allergenic subunits of glycinin. Compared with the alkaline chain, the acidic chain A2 of the G2 subunit has strong allergenicity. However, the precise epitopes of A2 and the epitopes destroyed during processing are still unknown. RESULTS: In the present study, preparation of two specific antibodies damaged by processing and phage display techniques were applied to locate the antigenic epitopes of glycinin A2 polypeptide chains disrupted by two processing techniques (thermal processing and ultra-high pressure combined thermal processing). Bioinformatics methods were used to predict the possible epitopes of the A2 chain. The A2 chain and its overlapping segments were introduced into T7 phages and expressed on phage shell by phage display. An indirect enzyme-linked immunosorbent assay was used to screen for antigenic epitopes that had been disrupted by the two processing technologies. The results showed that the dominant antigenic region disrupted by processing was located mainly in the A2-3-B fragment. The reacting experiment with the serum of allergic patients showed that the A2-3-B fragment protein was not only an antigenic region, but also an allergenic region. The two processing technologies destroyed the allergenic epitopes of A2 chain, thereby reducing the allergenicity of protein. The amino acids where the dominant allergenic region disrupted by processing was located were: 233 AIVTVKGGLRVTAPAMRKPQQEEDDDDEEEQPQCVE268 . CONCLUSION: Precise epitopes of the acidic chain A2 in glycinin were identified and epitopes destroyed in two common processing methods were also obtained. The application products of rapid detection of de-allergenicity effect of processed food can be developed according to the location of processed destruction allergenic region, which is of great significance with respect to preventing the occurrence of soybean allergenic diseases. © 2022 Society of Chemical Industry.

Predicting Antigenic Peptides from Rocio Virus NS1 Protein for Immunodiagnostic Testing Using Immunoinformatics and Molecular Dynamics Simulation.

The mosquito-borne disease caused by the Rocio virus is a neglected threat, and new immune inputs for serological testing are urgently required for diagnosis in low-resource settings and epidemiological surveillance. We used in silico approaches to identify a specific antigenic peptide (p_ROCV2) in the NS1 protein of the Rocio virus that was theoretically predicted to be stable and exposed on its surface, where it demonstrated key properties allowing it to interact with antibodies. These findings related to the molecular dynamics of this peptide provide important insights for advancing diagnostic platforms and investigating therapeutic alternatives.

Immunogenicity and Immunoprotection of PCV2 Virus-like Particles Incorporating Dominant T and B Cell Antigenic Epitopes Paired with CD154 Molecules in Piglets and Mice.

Porcine circovirus type 2 (PCV2) is capable of causing porcine circovirus-associated disease (PCVAD) and is one of the major threats to the global pig industry. The nucleocapsid protein Cap encoded by the PCV2 ORF2 gene is an ideal antigen for the development of PCV2 subunit vaccines, and its N-terminal nuclear localization sequence (NLS) structural domain is essential for the formation of self-assembling VLPs. In the present study, we systematically expressed and characterized full-length PCV2 Cap proteins fused to dominant T and B cell antigenic epitopes and porcine-derived CD154 molecules using baculovirus and found that the Cap proteins fusing epitopes were still capable of forming virus-like particles (VLPs). Both piglet and mice experiments showed that the Cap proteins fusing epitopes or paired with the molecular adjuvant CD154 were able to induce higher levels of humoral and cellular responses, particularly the secretion of PCV2-specific IFN-γ and IL-4. In addition, vaccination significantly reduced clinical signs and the viral load of PCV2 in the blood and tissues of challenged piglets. The results of the study provide new ideas for the development of a more efficient, safe and broad-spectrum next-generation PCV2 subunit vaccine.

Candidate antigenic epitopes for vaccination and diagnosis strategies of Toxoplasma gondii infection: A review.

Toxoplasmosis caused by an obligatory intracellular protozoan parasite of Toxoplasma gondii threats a wide spectrum of human and animal hosts. It has been shown that the intensity of the disease in humans depends on the host's immune responses. Immunological investigations on whole protein molecules of T. gondii have shown that these antigens are not fully responsible for the immune response, which leads to a decrease in specificity and affinity of the antigen (epitope)-antibody (paratope) binding. Currently, epitopes have shown promising entities to stimulate B, T, cytotoxic T lymphocyte, and NK cells resulting in enhancement of protective immunity against toxoplasmosis patients. Thus, the accurate designing, prediction, and conducting of antigenic epitopes of T. gondii (with linear and/or spatial structures (can augment our understanding about development of new serological diagnostic kits and vaccines. The current review provides an update on the latest advances of current epitopes described against toxoplasmosis including B cell/T cell epitopes, antigen types, parasite strains, epitope sequences, assay settings (in vitro and/or in vivo), and target strategy. Present results disclosed that the designing of effective multiepitopes of T. gondii by in silico modeling and immunoinformatics tools can strengthen our knowledge about triggering of epitope-based vaccine/diagnosis strategies in future perspectives.

Antigenic epitopes on the outer membrane protein A of Escherichia coli identified with single-chain variable fragment (scFv) antibodies.

Bacterial meningitis is a severe disease that is fatal to one-third of patients. The major cause of meningitis in neonates is Escherichia coli (E. coli) K1. This bacterium synthesizes an outer membrane protein A (OmpA) that is responsible for the adhesion to (and invasion of) endothelial cells. Thus, the OmpA protein represents a potential target for developing diagnostic and therapeutic agents for meningitis. In this study, we expressed recombinant OmpA proteins with various molecular weights in E. coli. The sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was performed to check the molecular size of OmpA's full length (FL) and truncated proteins. OmpA-FL protein was purified for immunizing chickens to produce immunoglobulin yolk (IgY) antibodies. We applied phage display technology to construct antibody libraries (OmpA-FL scFv-S 1.1 × 107 and OmpA-FL scFv-L 5.01 × 106) to select specific anti-OmpA-FL scFv antibodies; these were characterized by their binding ability to recombinant or endogenous OmpA using ELISA, immunofluorescent staining, and confirmed with immunoblotting. We found 12 monoclonal antibodies that react to OmpA fragments; seven scFvs recognize fragments spanning amino acid (aa) residues 1-346, aa 1-287, aa 1-167, and aa 60-192, while five scFvs recognize fragments spanning aa 1-346 and aa 1-287 only. Two fragments (aa 246-346 and aa 287-346) were not recognized with any of the 12 scFvs. Together, the data suggest three antigenic epitopes (60 aa-160 aa, 161 aa-167 aa, 193 aa-245 aa) recognized by monoclonal antibodies. These scFv antibodies show strong reactivity against OmpA proteins. We believe that antibodies show promising diagnostic agents for E. coli K1 meningitis.

How Computational Epitope Mapping Identifies the Interactions between Nanoparticles Derived from Papaya Mosaic Virus Capsid Proteins and Immune System.

BACKGROUND: Nanoparticles derived from plant viruses possess fascinating structures, versa-tile functions and safe properties, rendering them valuable for a variety of applications. Papaya mosaic Virus-Like Particles (VLPs) are nanoparticles that contain a repetitive number of virus capsid proteins (PMV-CP) and are considered to be promising platforms for vaccine design. Previous studies have re-ported the antigenicity of PMV nanoparticles in mammalian systems. MATERIALS AND METHODS: As experiments that concern vaccine development require careful design and can be time consuming, computational experiments are of particular importance. Therefore, prior to ex-pressing PMV-CP in E. coli and producing nanoparticles, we performed an in silico analysis of the virus particles using software programs based on a series of sophisticated algorithms and modeling networks as useful tools for vaccine design. A computational study of PMV-CP in the context of the immune sys-tem reaction allowed us to clarify particle structure and other unknown features prior to their introduc-tion in vitro. RESULTS: The results illustrated that the produced nanoparticles can trigger an immune response in the absence of fusion with any foreign antigen. CONCLUSION: Based on the in silico analyses, the empty capsid protein was determined to be recognised by different B and T cells, as well as cells which carry MHC epitopes.

Identification of common vaginal Lactobacilli immunoreactive proteins by immunoproteomic techniques.

Lactobacilli are considered as the most important microorganisms in regulating immune system and maintaining vaginal health. The uses and benefits of Lactobacilli as probiotics, particularly the regulation of immune system, are dependent on the strain used and a comprehensive understanding of their effects on the host. Several factors have been identified in Lactobacilli that influence the immune response, such as exopolysaccharides and proteins. The current study was designed to investigate the serum immunoreactivity of healthy women against common vaginal Lactobacilli immunoreactive proteins. Three common vaginal Lactobacillus strains (L. crispatus L1, L. gasseri L9, and L. fermentum L2) were compared for immune response. The ELISA results showed that the levels of total immunoglobulin (Ig-total) antibody for L. crispatus L1, L. fermentum L2, and L. gasseri L9 were 47%, 45% and 29%, respectively. Regarding the lower prevalence of L. fermentum L2 in comparison with the other two strains, the approximately equal levels of Ig-total compared to L. crispatus L1 and more than L. gasseri L9 indicate that L. fermentum L2 has the greater antigenicity ability. Accordingly, the immunoreactive proteins of L. fermentum L2 were identified using MALDI-TOF-MS detected by SDS-PAGE and Western blotting. These proteins included 30s ribosomal protein S4 and 50s ribosomal protein L5. Antigenic epitopes on the 3D structure of these proteins was also predicted using bioinformatics analysis. The presence of antibody in serum of healthy pre-menopausal women indicates that Lactobacilli (normal flora) proteins can stimulate host immune response. Purification and further studies of the proteins may allow their potential use as an adjuvant to improve the efficacy of vaccines.

Antigenic potential of a recombinant polyvalent DNA vaccine against pathogenic leptospiral infection.

Leptospirosis is a serious epidemic disease caused by pathogenic Leptospira species. The disease is endemic in most tropical and sub-tropical regions of the world. Currently, there is no effective polyvalent vaccine for prevention against most of the circulating serovars. Moreover, development of an efficient leptospiral vaccine capable of stimulating cross-protective immune responses against a wide range of serovars remains a daunting challenge. This, in part, is associated with the extensive diversity and variation of leptospiral serovars from region to region. In this study, a multi-epitope DNA vaccine encoding highly immunogenic epitopes from LipL32 and LipL41 was designed using in-silico approach. The DNA encoding antigenic epitopes was constructed from conserved pathogenic Leptospira genes (LipL32 and LipL41). Immunization of golden Syrian hamsters with the multi-epitope chimeric DNA vaccine resulted in the production of both agglutinating and neutralizing antibodies as evidence by MAT and in-vitro growth inhibition tests respectively. The antibodies produced reacted against eight different serovars and significantly reduced renal colonization following in vivo challenge. The vaccine was also able to significantly reduce renal colonization which is a very important factor responsible for persistence of leptospires among susceptible and reservoir animal hosts. In conclusion, the leptospiral multi-epitope chimeric DNA vaccine can serve as a potentially effective and safe vaccine against infection with different pathogenic leptospiral serovars.

Genetic analysis and characterization of wild poliovirus type 1 during sustained transmission in a population with >95% vaccine coverage, Israel 2013.

BACKGROUND: Israel has >95% polio vaccine coverage with the last 9 birth cohorts immunized exclusively with inactivated polio vaccine (IPV). Using acute flaccid paralysis and routine, monthly countrywide environmental surveillance, no wild poliovirus circulation was detected between 1989 and February 2013, after which wild type 1 polioviruses South Asia genotype (WPV1-SOAS) have persistently circulated in southern Israel and intermittently in other areas without any paralytic cases as determined by intensified surveillance of environmental and human samples. We aimed to characterize antigenic and neurovirulence properties of WPV1-SOAS silently circulating in a highly vaccinated population. METHODS: WPV1-SOAS capsid genes from environmental and stool surveillance isolates were sequenced, their neurovirulence was determined using transgenic mouse expressing the human poliovirus receptor (Tg21-PVR) mice, and their antigenicity was characterized by in vitro neutralization using human sera, epitope-specific monoclonal murine anti-oral poliovirus vaccine (OPV) antibodies, and sera from IPV-immunized rats and mice. RESULTS: WPV1 amino acid sequences in neutralizing epitopes varied from Sabin 1 and Mahoney, with little variation among WPV1 isolates. Neutralization by monoclonal antibodies against 3 of 4 OPV epitopes was lost. Three-fold lower geometric mean titers (Z = -4.018; P < .001, Wilcoxon signed-rank test) against WPV1 than against Mahoney in human serum correlated with 4- to 6-fold lower neutralization titers in serum from IPV-immunized rats and mice. WPV1-SOAS isolates were neurovirulent (50% intramuscular paralytic dose in Tg21-PVR mice: log10(7.0)). IPV-immunized mice were protected against WPV1-induced paralysis. CONCLUSIONS: Phenotypic and antigenic profile changes of WPV1-SOAS may have contributed to the intense silent transmission, whereas the reduced neurovirulence may have contributed to the absence of paralytic cases in the background of high population immunity.

Comparative analysis of the RVA VP7 and VP4 antigenic epitopes circulating in Iran and the Rotarix and RotaTeq vaccines.

Analyzing the lineages and detecting antigenic variation in immunogenic motifs of Group A Rotavirus (RVA) variants is crucial because it can impact vaccine efficacy. This study investigated the circulating lineages of VP4 and VP7 proteins of human RVA isolates and their phylogeny in ≤24-month-old symptomatic, rotavirus-positive children with transudative diarrhea within 48 h of admission to Mofid Children's Hospital between December 2020 and March 2022 in Tehran, Iran. Antigen detection was performed by ELISA, RNA extraction, and semi-nested multiplex PCR for G/P genotypes, followed by sequencing and bioinformatic analysis using multiple sequence alignments in MEGA and phylogenetic analysis by Geneious Prime. The similarity of VP7 and VP4 amino acids with the RotaTeq and Rotarix vaccine strains for cytotoxic T cell and antigenic epitopes was evaluated using the UCSF Chimera Molecular Modeling System. Overall, 27.3 % of the samples were RVA positive, showing untypeable (2.5 %), single (76.9 %), and mixed (20.5 %) genotypic characteristics. The strains clustered in the G1/II, G2/IV, G3/I, G4/I, G9/III, P (Kachooei et al., 2023) [8]/III, P (Howley et al., 2020) [4]/V, and P (Wahyuni et al., 2021) [6]/I lineages. Comparative analysis of VP7 antigenic epitopes showed that the G1/II strains were completely conserved, while the G2/IV, G3/I, G4/I, G6, G9/III strains contained 2, 3-5, 2, 4 and 9 amino acid substitutions, respectively. The P (Kachooei et al., 2023) [8]/III genotypes differed by 3 amino acids, while the P (Wahyuni et al., 2021) [6]/I genotype had the most substitutions. CTL epitopes were completely conserved in G3/I strains, but other genotypes differed by 1-4 amino acids compared to the vaccine strains. Given the diversity of circulating RVA genotypes and the observed mutations in neutralizing and CTL epitopes, immune escape by some of the strains is likely in Iran. This finding underscores the importance of evaluating the effect of rotavirus vaccines on local genotypes and related lineages before implementing a vaccination program.

Immunoinformatics approach for design novel multi-epitope prophylactic and therapeutic vaccine based on capsid proteins L1 and L2 and oncoproteins E6 and E7 of human papillomavirus 16 and human papillomavirus 18 against cervical cancer.

BACKGROUND: This study aimed to identify the optimal protein construction for designing a multi-epitope vaccine with both prophylactic and therapeutic effects against cervical cancer, utilizing an immunoinformatics approach. The construction process involved using capsid epitopes L1 and L2, as well as oncoproteins E5, E6, and E7 from human papillomavirus (HPV) types 16 and 18. METHODS: An experimental in silico analysis with an immunoinformatics approach was used to develop 2 multi-epitope vaccine constructs (A and B). Further analysis was then conducted to compare the constructs and select the one with the highest potential against cervical cancer. RESULTS: This study produced 2 antigenic, non-allergenic, and nontoxic multi-epitope vaccine constructs (A and B), which exhibited the ideal physicochemical properties for a vaccine. Further analysis revealed that construct B effectively induced both cellular and humoral immune responses. CONCLUSION: The multi-epitope vaccine construct B for HPV 16 and 18, designed for both prophylactic and therapeutic purposes, met the development criteria for a cervical cancer vaccine. However, these findings need to be validated through in vitro and in vivo experiments.

Exploring the S Protein of SARS-CoV-2 to Design a Novel Multi-Epitope Vaccine against COVID-19 Based on Immunoinformatics Approaches.

BACKGROUND: Developing a novel COVID-19 multi-epitope vaccine (CoVMEV) is essential to containing the SARS-CoV-2 pandemic. METHODS: The virus's immunodominant B and T cell epitopes from the S protein were found and joined to create the CoVMEV. Bioinformatics techniques were used to investigate the secondary and tertiary structures, as well as the physical and chemical properties of CoVMEV. RESULTS: CoVMEV exhibited high antigenicity and immunogenicity scores, together with good water solubility and stability. Toll-like receptor 2 (TLR2) and toll-like receptor4 (TLR4), which are critical in triggering immunological responses, were also strongly favoured by CoVMEV. Molecular dynamics simulation and immune stimulation studies revealed that CoVMEV effectively activated T and B lymphocytes, and increased the number of active CD8+ T cells than similar vaccines. CONCLUSION: CoVMEV holds promise as a potential vaccine candidate for COVID-19, given its robust immunogenicity, stability, antigenicity, and capacity to stimulate a strong immune response. This study presents a significant design concept for the development of peptidyl vaccines targeting SARS-CoV-2. Further investigation and clinical trials will be crucial in assessing the efficacy and safety of CoVMEV as a potential vaccine for COVID-19.

Corrigendum: Phylogenetic analysis of the viral proteins VP4/VP7 of circulating human rotavirus strains in China from 2016 to 2019 and comparison of their antigenic epitopes with those of vaccine strains.

[This corrects the article DOI: 10.3389/fcimb.2022.927490.].

Study on the Sensitization and Antigenic Epitopes of Tropomyosin from Antarctic Krill (Euphausia superba).

Antarctic krill (Euphausia superba), a shrimp-like marine crustacean, has become a beneficial source of high-quality animal protein. Meanwhile, a special focus has been placed on its potential sensitization issue. In this study, a 35 kDa protein was purified and identified to be Antarctic krill tropomyosin (AkTM) by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The purified TM showed a strong IgE-binding capacity to shrimp/crab-allergic patients' sera, indicating that TM is the primary allergen in Antarctic krill. Simulated gastrointestinal digestion revealed that the digestion stability of TM to pepsin was higher than that to trypsin. The strong degranulation triggered by TM in RBL-2H3 cells suggested that AkTM has a strong sensitization capacity. The TM-sensitized BALB/c mice displayed severe anaphylactic symptoms; high levels of TM-specific IgE, sIgG1, and histamine; and increased IL-4, indicating that AkTM could provoke IgE-mediated allergic reactions. Bioinformatics prediction, indirect competition ELISA, and mast cell degranulation assay were used to map the antigenic epitopes of AkTM. Finally, nine peptides of T43-58, T88-101, T111-125, T133-143, T144-155, T183-197, T223-236, T249-261, and T263-281 were identified as the linear epitopes of AkTM. The findings may help us develop efficient food processing techniques to reduce krill allergy and gain a deeper comprehension of the allergenicity of krill allergens.

Electron beam irradiation degrades the toxicity and alters the protein structure of Staphylococcus aureus alpha-hemolysin.

α-Hemolysin (Hla) is a potent pore-forming toxin (PFT) produced by Staphylococcus aureus that exacerbates the pathogenesis of S. aureus enterotoxicity and plays a role in population food poisoning. Hla lyses cells by binding to host cell membranes and oligomerizing to form heptameric structures, thereby disrupting the cell barrier. Although the broad bactericidal effect of electron beam irradiation (EBI) has been demonstrated whether it has a damaging or degrading effect on Hla's remains unknown. In this study, EBI was found to have the effect of altering the secondary structure of Hla proteins, verifying that the damaging effect of EBI-treated Hla on intestinal and skin epithelial cell barriers was significantly reduced. It was noted by hemolysis and protein interactions that EBI treatment significantly disrupted the binding of Hla to its high-affinity receptor, but did not affect the binding between Hla monomers to form heptamers. Thus, EBI can effectively reduce the threat of Hla to food safety.

Designing a bioadjuvant candidate vaccine targeting infectious bursal disease virus (IBDV) using viral VP2 fusion and chicken IL-2 antigenic epitope: A bioinformatics approach.

Infectious Bursal Disease (IBD) is a common and contagious viral infection that significantly affects the poultry industry. This severely suppresses the immune system in chickens, thereby threating their health and well-being. Vaccination is the most effective strategy for preventing and controlling this infectious agent. The development of VP2-based DNA vaccines combined with biological adjuvants has recently received considerable attention due to their effectiveness in eliciting both humoral and cellular immune responses. In this study, we applied bioinformatics tools to design a fused bioadjuvant candidate vaccine from the full-length sequence of the VP2 protein of IBDV isolated in Iran using the antigenic epitope of chicken IL-2 (chiIL-2). Furthermore, to improve the antigenic epitope presentation and to maintain the three-dimensional structure of the chimeric gene construct, the P2A linker (L) was used to fuse the two fragments. Our in-silico analysis for the design of a candidate vaccine indicates that a continuous sequence of amino acid residues ranging from 105 to 129 in chiIL-2 is proposed as a B cell epitope by epitope prediction servers. The final 3D structure of the VP2-L-chiIL-2105-129 was subjected to physicochemical property determination, molecular dynamic simulation, and antigenic site determination. The results of these analyses led to the development of a stable candidate vaccine that is non-allergenic and has the potential for antigenic surface display potential and adjuvant activity. Finally, it is necessary to investigate the immune response induced by our proposed vaccine in avian hosts. Notably, increasing the immunogenicity of DNA vaccines can be achieved by combining antigenic proteins with molecular adjuvants using the principle of rational vaccine design.

Pulsed Electric Field-Assisted Alcalase Treatment Reduces the Allergenicity and Eliminates the Antigenic Epitopes of Ovomucoid.

Physically assisted chemical modifications can effectively reduce the allergenicity of ovomucoid (OVM). However, only a few studies have used pulsed electric field (PEF)-assisted alcalase hydrolysis to reduce the allergenicity of OVM. Herein, we investigated the effect of PEF-assisted alcalase treatment on the spatial conformation, allergenicity, and antigenic epitopes of OVM based on multispectroscopic analyses, bioinformatics, and mass spectrometry. The results showed that PEF-assisted alcalase treatment promoted the hydrolysis of OVM; moreover, the α-helix content and surface hydrophobicity of OVM significantly decreased, which disordered its spatial conformation and weakened its intermolecular interactions. Additionally, enzyme-linked immunosorbent assay (ELISA) results showed that the PEF-assisted alcalase treatment significantly reduced the binding levels of IgE and IgG1, which were 47.66 and 36.41%, respectively. Finally, eight epitopes of OVM were obtained by immunoinformatic tools. Nano-high performance liquid chromatography coupled to tandem mass spectrometry (nano-HPLC MS/MS) results showed that the hydrolysate of OVM and alcalase (HOVM) had nine more peptide-containing epitopes than the hydrolysate of PEF-treated OVM and PEF-treated alcalase (HOVM-PP'), indicating that PEF could promote the elimination of linear epitopes in OVM, thereby reducing OVM allergenicity.

TPBTE: A model based on convolutional Transformer for predicting the binding of TCR to epitope.

T cell receptors (TCRs) selectively bind to antigens to fight pathogens with specific immunity. Current tools focus on the nature of amino acids within sequences and take less into account the nature of amino acids far apart and the relationship between sequences, leading to significant differences in the results from different datasets. We propose TPBTE, a model based on convolutional Transformer for Predicting the Binding of TCR to Epitope. It takes epitope sequences and the complementary decision region 3 (CDR3) sequences of TCRß chain as inputs. And it uses a convolutional attention mechanism to learn amino acid representations between different positions of the sequences based on learning local features of the sequences. At the same time, it uses cross attention to learn the interaction information between TCR sequences and epitope sequences. A comprehensive evaluation of the TCR-epitope data shows that the average area under the curve of TPBTE outperforms the baseline model, and demonstrate an intentional performance. In addition, TPBTE can give the probability of binding TCR to epitopes, which can be used as the first step of epitope screening, narrowing the scope of epitope search and reducing the time of epitope search.

Ferritin Light Chain: A Candidate Autoantigen in Immuno-Related Pancytopenia.

The characteristic feature of immune-related pancytopenia (IRP) is autoantibody-mediated bone marrow (BM) damage and peripheral blood cytopenia. We found that the potential antigen of IRP was Ferritin light chain (FTL) by SEREX (serological analysis of recombinant cDNA expression libraries) in the previous study. In this study, we tried to explore the antigenic epitopes of FTL and verify its antigenicity in IRP. We found the possible FTL epitope: VNLYLQASYTYLSLG by phage random peptide library. Through ELISPOT, it was found that peptide VNLYLQASYTYLSLG can significantly stimulate the production of interleukin-4 and cannot stimulate the production of interferon-γ, which suggested that the peptide can obviously activate Th2 cells. Peptide-major histocompatibility complex tetramer elicited antigen-specific T cell responses. The expression levels of FTL were significantly increased in the patients with untreated IRP (P < 0.05). In conclusion, we found that FTL is the target antigen for some patients with IRP. The peptide of VNLYLQASYTYLSLG is an epitope of the target antigen. The target antigen is abnormally overexpressed on the membrane of BM cells, especially on the surface of CD34+ BM cells of patients with IRP. In addition, it is related to the severity of disease. These results provide a possible new target for the treatment of IRP in the future.