Antigen epitopes of animal coronaviruses:a mini-review

Coronaviruses are widespread in nature and can infect mammals and poultry,making them a public health concern.Globally,prevention and control of emerging and re-emerging animal coronaviruses is a great challenge.The mecha-nisms of virus-mediated immune responses have important implications for research on virus prevention and control.The antigenic epitope is a chemical group capable of stimulating the production of antibodies or sensitized lympho-cytes,playing an important role in antiviral immune responses.Thus,it can shed light on the development of diagnos-tic methods and novel vaccines.Here,we have reviewed advances in animal coronavirus antigenic epitope research,aiming to provide a reference for the prevention and control of animal and human coronaviruses.

Recent advances in the study of epitopes,allergens and immunologic cross-reactivity of edible mango

Mango(Mangifera indica L.)is a tropical fruit that is widely consumed as both fresh fruits and processed products around the world.The high incidence of mango allergy,on the other hand,has sparked widespread concern.Therefore,a summary and analysis of the current status and issues in mango allergen research can guide in-depth study on the mechanism of mango allergy and reveal effective desensitization methods.We described the incidence of fruit allergy,as well as the mechanism and clinical symptoms of mango allergy,in this review.We also looked into the structural properties of mango allergens,the effect of processing methods on mango allergens,prediction methods for mango allergen epitopes,and the current state of research on mango cross-reactive allergens and preventive measures.Finally,the research directions and ideas for the future are proposed and discussed.

Bioinformatics analysis of the structure and linear B-cell epitopes of aquaporin-3 from Schistosoma japonicum

Objective:To analyze the structure of aquaporins-3(AQP-3) from Schistosoma japonicum(SJAQP-3) using bioinformalical methods,and to provid of references for vaccine targets research.Methods:Protparam,BepiPred,TMHMM Server,MLRC,Geno3d,DNA star software packages were used to predict the physical and chemical properties,hydrophilicity plot, flexibility regions,antigenic index,surface probability plot,secondary structure,and tertiary structure of amino acid sequence of SJAQP-3.Results:SJAQP-3 had six transmembrane regions and two half-spanning helices that form a central channel.The half-spanning helices fold into the centre of the channel.Either of the half-spanning helix had a conserved motif of NPA common to all aquaporins.Predicted linear B-Cell epitopes were most likely at the N-terminal amino acid residues of Saa-7aa,59aa- 62aa,225aa-230aa,282aa -288aa,294aa -29Saa and 305aa -307aa area.59aa- 62aa,22Saa-230aa located outside the membrane,the others located inside the cell.Conclusions:SJAQP-3 is a integral membrane protein in Schistosoma japonicum tegument.There are six potential epitopes in SJ AQP-3.It might be a potential molecular target for the development of vaccines.

Helicobacter pylori specific immune response induced by conservative flagellin linear B-cell epitope

AIM:To testify the immunogenicity of a conservative B-cell linear epitope of Helicobacter pylori ( H pylori) flagellin A. METHODS: Different programs were used to analyze the secondary structure, molecular hydropathy, and surface accessibility of Hpyloriflagellin A. Linear B-cell epitopes were estimated based on the structural and physiochemical information. Analysis of residue divergence was proposed to screen a conservative linear epitope. The 29-peptide (Pep29mer) synthesized by chemical method, including the predicted conservative B-cell epitope and a known K^2d compatible T-cell epitope, was used to immunize mice, and then H pylori-specific antibodies were detected by ELISA. RESULTS: Based on the analyses of divergent amino acid residues, structural and physiochemical characteristics, it was strongly suggested that the short fragment NDSDGR was the core of a conservative linear epitope in flagellin A. Animals immunized by Pep29mer acquired efficient immune response. In detail, serum Hpylori-specific IgA and IgGl increased significantly in immunized group, while IgG2a only had an insignificant change. Hpylori-specific IgA in gastrointestinal flushing fluid also increased significantly. CONCLUSION: The conservative short fragment NDSDGR is the core of a linear B-cell epitope of flagellin A.

Identification and epitope mapping of anti-p72 single-chain antibody against African swine fever virus based on phage display antibody library

African swine fever virus(ASFV)is a lethal pathogen that causes severe threats to the global swine industry and it has already had catastrophic socio-economic effects.To date,no licensed prophylactic vaccine exists.Limited knowledge exists about the major immunogens of ASFV and the epitope mapping of the key antigens.As such,there is a considerable requirement to understand the functional monoclonal antibodies(mAbs)and the epitope mapping may be of utmost importance in our understanding of immune responses and designing improved vaccines,therapeutics,and diagnostics.In this study,we generated an ASFV antibody phage-display library from ASFV convalescent swine PBMCs,further screened a specific ASFV major capsid protein(p72)single-chain antibody and fused with an IgG Fc fragment(scFv-83-Fc),which is a specific recognition antibody against ASFV Pig/HLJ/2018 strain.Using the scFv-83-Fc mAb,we selected a conserved epitope peptide(221MTGYKH226)of p72 retrieved from a phage-displayed random peptide library.Moreover,flow cytometry and cell uptake experiments demonstrated that the epitope peptide can significantly promote BMDCs maturation in vitro and could be effectively uptaken by DCs,which indicated its potential application in vaccine and diagnostic reagent development.Overall,this study provided a valuable platform for identifying targets for ASFV vaccine development,as well as to facilitate the optimization design of subunit vaccine and diagnostic reagents.

The amino acids differences in epitopes may promote the different allergenicity of ovomucoid derived from hen eggs and quail eggs

Quail egg ovomucoid can inhibit activation of basophils and eosinophils,while hen egg ovomucoid has been shown to be a major allergen,named Gal d 1.At present,the differences in structure and function between two ovomucoid are unclear.We found the homology of ovomucoid in quail eggs and hen eggs reached77%.Compared with hen egg ovomucoid,the distribution of secondary structure was different in AA52-53,AA57-58,AA66-68,AA71-72,AA131-133,AA139-140,AA157-159 and AA184-185.Among 9 epitopes of egg ovomucoid,there were different amino acids from quail egg ovomucoid in 8 epitopes.Recombination quail egg ovomucoid had trypsin inhibition activity and quail egg ovomucoid didn't specifically bind to serum of eggs allergic patients.Quail egg ovomucoid can significantly inhibit RBL-2 H3 cells degranulation and protect cells morphology to a certain extent,indicating quail egg ovomucoid can inhibit cells activation and have potential anti-allergic effects,which is related to trypsin inhibitory activity.The difference in sensitization compare to hen egg ovomucoid may be due to amino acids differences affecting protein structure by changing antigenic epitopes.

An Improved Method for Predicting Linear B-cell Epitope Using Deep Maxout Networks

To establish a relation between an protein amino acid sequence and its tendencies to generate antibody response,and to investigate an improved in silico method for linear B-cell epitope（LBE）prediction.We present a sequence-based LBE predictor developed using deep maxout network（DMN）with dropout training techniques.A graphics processing unit（GPU）was used to reduce the training time of the model.A 10-fold cross-validation test on a large,non-redundant and

Rapid, accurate and serotype independent pipeline for in silico epitope mapping of SARS-CoV-2 antigens: a combined machine learning and Chou’s pseudo amino acid composition method

Here,a new integrated machine learning and Chou’s pseudo amino acid composition method has been proposed for in silico epitope mapping of severe acute respiratorysyndrome-like coronavirus antigens.For this,a training dataset including 266 linear B-cell epitopes,1,267 T-cell epitopes and 1,280 non-epitopes were prepared.The epitope sequences were then converted to numerical vectors using Chou’s pseudo amino acid composition method.The vectors were then introduced to the support vector machine,random forest,artificial neural network,and K-nearest neighbor algorithms for the classification process.The algorithm with the highest performance was selected for the epitope mapping procedure.Based on the obtained results,the random forest algorithm was the most accurate classifier with an accuracy of 0.934 followed by K-nearest neighbor,artificial neural network,and support vector machine respectively.Furthermore,the efficacies of predicted epitopes by the trained random forest algorithm were assessed through their antigenicity potential as well as affinity to human B cell receptor and MHC-I/II alleles using the VaxiJen score and molecular docking,respectively.It was also clear that the predicted epitopes especially the B-cell epitopes had high antigenicity potentials and good affinities to the protein targets.According to the results,the suggested method can be considered for developing specific epitope predictor software as well as an accelerator pipeline for designing serotype independent vaccine against the virus.

Theoretical Study of Continuous B-Cell Epitopes with Developed BP Neural Network

In order to identify continuous B-cell epitopes effectively and to increase the success rate of experimental identification, the modified Back Propagation artificial neural network (BP neural network) was used to predict the continuous B-cell epitopes, and finally the predictive model for the B-cells epitopes was established. Comparing with the other predictive models, the prediction performance of this model is more excellent (AUC = 0.723). For the purpose of verifying the performance of the model, the prediction to the SWISS PROT NUMBER: P08677 was carried on, and the satisfying results were obtained.

B-cell epitope mapping of human testis specific basic protein

Sesum from an immunologically infertile patient (ISA-I) was used in screening human testis cDNA expression library. A new testis--specific candidate antigen-- human testis specific basic protein (TSBP) was identified by this patient serum. DNA sequencing and homology searching in databases showed that TSBP is a new testis specific protein. Northern blot analyses showed that TSBP recognized a single message present only in testis. The fusion protein expressed in E. Colt was recognized by original serum ISA--I. A B cell epitope was identified in region of 11 amino acid residues near the carboxyterminus of the TSBP protein by unidirectional nested deletion method and Western blot analyses. A chimeric peptide containing the predicted epitope has been designed and synthesized.

Preclinical evaluation of cyclophosphamide and fludarabine combined with CD19 CAR-T in the treatment of B-cell hematologic malignancies in vivo

Background:Chimeric antigen receptor T(CAR-T)cell therapy has achieved marked therapeutic success in ameliorating hematological malignancies.However,there is an extant void in the clinical guidelines concerning the most effective chemotherapy regimen prior to chimeric antigen receptor T(CAR-T)cell therapy,as well as the optimal timing for CAR-T cell infusion post-chemotherapy.Materials and Methods:We employed cell-derived tumor xenograft(CDX)murine models to delineate the optimal pre-conditioning chemotherapy regimen and timing for CAR-T cell treatment.Furthermore,transcriptome sequencing was implemented to identify the therapeutic targets and elucidate the underlying mechanisms governing the treatment regimen.Results:Our preclinical in vivo evaluation determined that a combination of cyclophosphamide and fludarabine,followed by the infusion of CD19 CAR-T cells five days subsequent to the chemotherapy,exerts the most efficacious therapeutic effect in B-cell hematological malignancies.Concurrently,RNA-seq data indicated that the therapeutic efficacy predominantly perturbs tumor cell metabolism,primarily through the inhibition of key mitochondrial targets,such as C-Jun Kinase enzyme(C-JUN).Conclusion:In summary,the present study offers critical clinical guidance and serves as an authoritative reference for the deployment of CD19 CAR-T cell therapy in the treatment of B-cell hematological malignancies.

RPRD1B/CREPT facilitates the progression of diffuse large B-cell lymphoma by inhibiting apoptosis through the NF-κB signaling pathway

Objective:To investigate the role of RPRD1B in the progression of diffuse large B-cell lymphoma(DLBCL)and its potential as a therapeutic target.Methods:This study analyzed RPRD1B expression in DLBCL and normal tissues using public databases and assessed its prognostic impact through survival analysis.In vitro and in vivo experiments were conducted to explore the mechanisms by which RPRD1B influences tumor growth and apoptosis.Results:RPRD1B expression was significantly elevated in DLBCL compared to normal tissues and was associated with poor prognosis.In vitro and in vivo experiments demonstrated that RPRD1B promoted lymphoma cell proliferation and inhibited apoptosis through the NF-κB signaling pathway.Conclusions:RPRD1B plays a critical role in the progression of DLBCL by modulating apoptosis and cellular proliferation.Targeting RPRD1B may offer a novel therapeutic strategy for DLBCL,suggesting its potential as a prognostic marker and therapeutic target in hematological malignancies.

Genome-wide comparison inferred the origin and evolution of B-cell epitopes on the proteins of human influenza A virus

The novel strain H1N1 caused the outbreak of first pandemic influenza in 21 century. Now it is a common component of current seasonal influenza viruses. The recent transmission and plentiful genome sequences available provided a good opportunity to study the origin and evolution of epitopes on the proteins of human influenza virus. In the present study, the B-cell epitope compositions in the pandemic strains, circulating traditional seasonal strains, swine strains as well as highly virulent avian strain H5N1 were identified with the aid of the Immune Epitope DataBase (IEDB) and were compared at genomic level. A total of 14210 distinct sequences down-loaded from NCBI database were used for analysis. Some epitopes on proteins HA or NA, not conserved in recent seasonal strains, were found in 2009 pandemic strains but existed in the early human strains (1919-1935). The pandemic strain shared higher conserved epitopes with “bird flu” virus H5N1than classic human seasonal strains. The epitopes that could exist at common antigenic regions of HA protein are needed to further identify. The genetic exchanges between human and swine population by transmission was very active but the princepal side of the transmission could be from swine to human. These results provided valuable information on influenza A virus evolution and transmission by means of epitope analysis at genomic level.

Identifying relevant factors influencing cancer-related fatigue in patients with diffuse large B-cell lymphoma during chemotherapy

BACKGROUND Diffuse large B-cell lymphoma(DLBCL)is a rapidly growing malignant tumor,and chemotherapy is one of the treatments used to combat it.Although advancements of science and technology have resulted in more and more patients being able to receive effective treatment,they still face side effects such as fatigue and weakness.It is important to thoroughly investigate the factors that contribute to cancer-related fatigue(CRF)during chemotherapy.AIM To explore the factors related to CRF,anxiety,depression,and mindfulness levels in patients with DLBCL during chemotherapy.METHODS General information was collected from the electronic medical records of eligible patients.Sleep quality and mindfulness level scores in patients with DLBCL during chemotherapy were evaluated by the Pittsburgh Sleep Quality Index and Five Facet Mindfulness Questionnaire-Short Form.The Piper Fatigue Scale was used to evaluate the CRF status.The Self-Rating Anxiety Scale and Self-Rating Depression Scale were used to evaluate anxiety and depression status.Univariate analysis and multivariate regression analysis were used to investigate the factors related to CRF.RESULTS The overall average CRF level in 62 patients with DLBCL during chemotherapy was 5.74±2.51.In 25 patients,the highest rate of mild fatigue was in the cognitive dimension(40.32%),and in 35 patients the highest moderate fatigue rate in the behavioral dimension(56.45%).In the emotional dimension,severe fatigue had the highest rate of occurrence,34 cases or 29.03%.The CRF score was positively correlated with cancer experience(all P<0.01)and negatively correlated with cancer treatment efficacy(all P<0.01).Tumor staging,chemotherapy cycle,self-efficacy level,and anxiety and depression level were related to CRF in patients with DLBCL during chemotherapy.CONCLUSION There was a significant correlation between CRF and perceptual control level in patients.Tumor staging,chemotherapy cycle,self-efficacy level,and anxiety and depression level influenced CRF in patients with DLBCL during chemotherapy.

Primary anaplastic lymphoma kinase-positive large B-cell lymphoma of the left bulbar conjunctiva: A case report

BACKGROUND Anaplastic lymphoma kinase(ALK)-positive large B-cell lymphoma(LBCL)is an aggressive and rare variant of diffuse LBCL.Herein,we report an uncommon case of stage IE extranodal ALK-positive LBCL initially originating in the bulbar con-junctiva.CASE SUMMARY A 63-year-old woman presented with a mass in the left bulbar conjunctiva that had persisted for six months,accompanied by swelling and pain that had per-sisted for 3 d.Eye examination revealed an 8 mm slightly elevated pink mass in the lower conjunctival sac of the left eye.Microscopically,the tumor was com-posed of large immunoblastic and plasmablastic large lymphoid cells with scattered anaplastic or multinucleated large cells.Immunophenotypically,the neoplastic cells were positive for ALK,CD10,CD138,Kappa,MUM1,BOB.1,OCT-2,CD4,CD45,EMA,CD79a,CD38,and AE1/AE3,and negative for CD20,PAX5,Lambda,BCL6,CD30 and all other T-cell antigens.The results of gene rearrangement tests showed monoclonal IGH/IGK/IGL and TCRD rearran-gements.Fluorescence in situ hybridization studies did not reveal any BCL2,BCL6 or MYC rearrangements.Furthermore,Epstein-Barr virus was not detected by in situ hybridization in the lesions.Based on the histopathological and imaging examinations,the neoplasm was classified as stage IE ALK-positive LBCL.No further treatments were administered.At the 6,15,and 21 mo postoperative follow-up visits,the patient was in good condition,without obvious discomfort.This case represents the first example of primary extranodal ALK-positive LBCL presenting as a bulbar conjunctival mass,which is extremely rare and shares morphological and immunohistochemical features with a variety of other neo-plasms that can result in misdiagnosis.CONCLUSION Awareness of the condition presented in this case report is necessary for early and accurate diagnosis and appropriate treatment.

Novel PIKfyve/Tubulin Dual-target Inhibitor as a Promising Therapeutic Strategy for B-cell Acute Lymphoblastic Leukemia

Objective:In B-cell acute lymphoblastic leukemia(B-ALL),current intensive chemotherapies for adult patients fail to achieve durable responses in more than 50%of cases,underscoring the urgent need for new therapeutic regimens for this patient population.The present study aimed to determine whether HZX-02-059,a novel dual-target inhibitor targeting both phosphatidylinositol-3-phosphate 5-kinase(PIKfyve)and tubulin,is lethal to B-ALL cells and is a potential therapeutic for B-ALL patients.Methods:Cell proliferation,vacuolization,apoptosis,cell cycle,and in-vivo tumor growth were evaluated.In addition,Genome-wide RNA-sequencing studies were conducted to elucidate the mechanisms of action underlying the anti-leukemia activity of HZX-02-059 in B-ALL.Results:HZX-02-059 was found to inhibit cell proliferation,induce vacuolization,promote apoptosis,block the cell cycle,and reduce in-vivo tumor growth.Downregulation of the p53 pathway and suppression of the phosphoinositide 3-kinase(PI3K)/AKT pathway and the downstream transcription factors c-Myc and NF-κB were responsible for these observations.Conclusion:Overall,these findings suggest that HZX-02-059 is a promising agent for the treatment of B-ALL patients resistant to conventional therapies.

SENEX-mediated CDK4/6 inhibition promotes senescence and confers apoptosis resistance in B-cell non-Hodgkin lymphoma

Background:The primary cause of treatment failure in patients with refractory or relapsed B-cell non-Hodgkin lymphoma(r/r B-NHL)is resistance to current therapies,and therapy-induced senescence(TIS)stands out as a crucial mechanism contributing to tumor drug resistance.Here,we analyzed SENEX/Rho GTPase Activating Protein 18(ARHGAP18)expression and prognostic significance in doxorubicin-induced B-NHL-TIS model and r/r B-NHL patients,investigating its target in B-NHL cell senescence and the effect of combining specific inhibitors on apoptosis resistance in B-NHL-TIS cells.Methods:Raji cells were transfected with the human SENEX shRNA recombinant lentiviral vector(Sh-SENEX)and the empty vector negative(NC)to construct a stable transfection cell line with knockdown of SENEX.Effect of SENEX-silencing on B-NHL-TIS formation,cell function and cell cycle-related pathways was analyzed.Using doxorubicin(DOX)-inducible senescent B-NHL cells combined with the specific cyclin dependent kinase 4/6(CDK4/6)inhibitor Palbociclib to observe that blocking CDK4/6 effects on TIS formation.SENEX expression of 21 B-NHL patients and 8 healthy controls were analyzed by qRT-PCR,and the correlation between its expression and clinical indicators were evaluated.Results:The downregulation of SENEX expression promotes G1-S phase transition and apoptosis while inhibiting cell proliferation,collectively suppressing the formation of TIS in B-NHL.Blockade of CDK4/6 promotes the DOX-induced G1 phase arrest to enhance TIS formation in B-NHL cells which can reverse the regulatory effect of silencing SENEX on B-NHL cell cycle regulation and senescence.The expression levels of SENEX were notably elevated in B-NHL patients compared to healthy controls,and Elevated expression levels of SENEX were associated with poor prognosis of B-NHL patients.Conclusions:SENEX enhances apoptosis resistance in B-NHL by inhibiting CDK4/6,thereby preventing G1-S phase transition and promoting TIS formation.

Transformation of marginal zone lymphoma into high-grade B-cell lymphoma expressing terminal deoxynucleotidyl transferase:A case report

BACKGROUND High-grade B-cell lymphoma(HGBL)is an unusual malignancy that includes myelocytomatosis viral oncogene(MYC),B-cell lymphoma-2(BCL-2),and/or BCL-6 rearrangements,termed double-hit or triple-hit lymphomas,and HGBL-not otherwise specific(HGBL-NOS),which are morphologically characteristic of HGBL but lack MYC,BCL-2,or BCL-6 rearrangements.HGBL is partially transformed by follicular lymphoma and other indolent lymphoma,with few cases of marginal zone lymphoma(MZL)transformation.HGBL often has a poor prognosis and intensive therapy is currently mainly advocated,but there is no good treatment for these patients who cannot tolerate chemotherapy.CASE SUMMARY We reported a case of MZL transformed into HGBL-NOS with TP53 mutation and terminal deoxynucleotidyl transferase expression.Gene analysis revealed the gene expression profile was identical in the pre-and post-transformed tissues,suggesting that the two diseases are homologous,not secondary tumors.The chemotherapy was ineffective and the side effect was severe,so we tried combination therapy including venetoclax and obinutuzumab.The patient tolerated treatment well,and reached partial response.The patient had recurrence of hepatocellular carcinoma and died of multifunctional organ failure.He survived for 12 months after diagnosis.CONCLUSION Venetoclax combined with obinutuzumab might improve the survival in some HGBL patients,who are unsuitable for chemotherapy.

Exact Location of Linear B-cell Epitopes of VP3 Protein of Goose Parvovirus

Four monoclonal antibodies (MAbs) against Goose Parvovirus (GPV) VP3 protein already available were used to precisely locate linear B-cell epitopes in VP3 of GPV. The epitopes, recognized by four MAbs, had already been identified at low levels of resolution. Complementary oligonucleotides encoding ten amino acid fragments, with five amino acid overlaps were designed with suitable sticky ends for recombination with pET-32a and subsequent expression as small-fragment fusion proteins. Antigenicity of specific oligopeptides was determined by Western blotting with the MAbs. Using the same methods, amino acids were deleted one by one from the peptides of interest, enabling the two epitopes to be precisely located at amino acids 430-435 (-DRIMNP-) and 643-647 (-VFIKN-).

鸭坦布苏病毒E蛋白特异性抗原表位鉴定及Epitope-ELISA血清学诊断方法建立

旨在建立鸭坦布苏病毒(DTMUV)的特异性血清学诊断方法。本研究以纯化的单克隆抗体1A5为固相筛选分子,利用噬菌体展示技术鉴定DTMUV囊膜(E)蛋白的特异性抗原表位,并利用DNAStar分析抗原表位序列在DTMUV中保守性和与其他黄病毒的E蛋白相应位点的氨基酸序列相似性。结果成功筛选到DTMUV E蛋白的一个线性抗原表位_(87)YAEYI_(91),该抗原表位在DTMUV中具有高度的保守性,无氨基酸位点差异,而与其他黄病毒E蛋白相应位点的氨基酸序列不具有相似性。Dot-Blotting结果表明表位_(87)YAEYI_(91)与DTMUV阳性血清具有良好的亲和性,而与JEV、DENV、WNV等黄病毒阳性血清间不出现交叉反应,可见抗原表位_(87)YAEYI_(91)为DTMUV所特有的抗原表位。利用DTMUV特异性抗原表位87YAEYI_(91)建立Epitope-ELISA血清学诊断方法并对126份鸭血清样品进行检测,以中和试验作为标准进行比较,结果显示Epitope-ELISA检测方法的相对特异性为100%,相对敏感度为96%,并且Epitope-ELISA与其他黄病毒血清间不出现交叉反应性,表明本研究建立的Epitope-ELISA检测方法是一种特异的、灵敏的ELISA血清学诊断方法。