Prediction of B Cell Epitope of DMRT Protein in Oreochromis niloticus

[Objective] The research aimed to predict the B cell epitope of DMRT protein in Oreochromis niloticus. [Method] The secondary structure of amino acid sequence of DMRT protein was revealed by Garnier-Robson, Chou-Fasman and Karplus-Schulz methods. The hydrophilicity plot, surface probability and antigenic index were obtained by Kyte-Doolittle, Emini and Jameson-Wolf methods, respectively. Based on the above results, the B cell epitopes for DMRT were predicted. [Result] Both the prediction results from Garnier-Robson, Chou-Fasman methods indicated that the α-helix centers of DMRT protein in O. niloticus were in the N terminal No. 31-56, 68-75, 110-116, 209-211 and 239-243; the β-sheet centers of DMRT protein in O. niloticus were in the N terminal No. 95-99, 177-183, 225-234 and 251-254. With the assistant of Kyte-Doolittle, Emini and Jameson-Wolf methods, the B cell epitopes for DMRT were located in or nearby the N terminal No. 13-16, 35-38, 47-54,84-93, 101-109, 127-156, 166-177 and 198-201. [Conclusion] These results are helpful for preparing the antibody of DMRT protein and revealing the sex determination mechanism of O. niloticus.

The Prediction of B Cell Epitopes for VP73 Protein of African Fever Virus

[Objective] The B cell epitopes for VP73 protein of African swine fever virus was predicted. [ Method] Based on the analysis of the amino acid sequence and the flexible regions of VP73 protein, the B cell epitopes for VP73 protein of African swine fever virus were predicted by method of Kyte-Doolittie, Emini and Jameson-Wolf. [Result] The B cell epitopes were located at or adjacent to the N-terminal No. 11 - 18,26 -48,73 -82,136 - 150,159 - 174,181 - 189,191 - 210,247 - 276,279 - 295,313 - 323 and 382 - 392. [Conclusion] The multi-parameters analytic method was adopted to predict the B cell epitopes for VP73 protein of African swine fever virus, which laid solid foundation for further characterizing the protein of VP73 and researching epitope vaccine.

Bioinformatics Analysis on B cell Epitopes of Rice Allergen RAG1

[Objective] To predict the secondary structure and B cell epitopes of the rice major allergen RAG1. [Method] The amino acid sequence of rice allergen RAG1 was acquired from Expasy protein database. The secondary structure of RAG1 was predicted by DNAStar Protean software with Gamier-Robson program, Chou-Fasman program and Karplus-Schulz program; the B cell epitopes of RAG1 was predicted with the Kyte Doolittle hydrophilic program, Emini surface accessibility program and Jameson-Wolf antigenic index program. [Result] The predictions on secondary structure and B cell epitopes showed that the regions of 33-44, 119-129, 155-163 were the dominant B cell epitopes. [Conclusion] This study predicted the potential dominant B cell epitopes in rice allergen RAG1 by comprehensive use of multi-methods and multi-parameters, and provided a theoretical basis for further researches on identification, antigen modification and epitope vaccine design of RAG1 B cell epitopes.

Prediction of T cell and B cell epitopes of the 22-, 47-, 56-, and 58-kDa proteins of Orientia tsutsugamushi

Objective:To predict B cell and T cell epitopes of 22-kDa,47-kDa,56-kDa and 58-kDa proteins.Methods:The sequences of 22-kDa,47-kDa,56-kDa and 58-kDa proteins which were derived from Orientia tsutsugamushi were analyzed by SOPMA,DNAstar,Bcepred,ABCpred,NetMHC,NetMHCⅡand IEDB.The 58-kDa tertiary structure model was built by MODELLER9.17.Results:The 22-kDa B-cell epitopes were located at positions 194-200,20-26 and 143-154,whereas the T-cell epitopes were located at positions 154-174,95-107,17-25 and 57-65.The 47-kD a protein B-cell epitopes were at positions 413-434,150-161 and 283-322,whereas the T-cell epitopes were located at positions 129-147,259-267,412-420 and 80-88.The 56-kDa protein B-cell epitopes were at positions 167-173,410-419 and 101-108,whereas the T-cell epitopes were located at positions 88-104,429-439,232-240 and 194-202.The 58-kDa protein B-cell epitopes were at positions 312-317,540-548 and 35-55,whereas the T-cell epitopes were located at positions 415-434,66-84 and 214-230.Conclusions:We identified candidate epitopes of 22-kDa,47-kDa,56-kDa and 58-kDa proteins from Orientia tsutsugamushi.In the case of 58-kDa,the dominant antigen is displayed on tertiary structure by homology modeling.Our findings will help target additional recombinant antigens with strong specificity,high sensitivity,and stable expression and will aid in their isolation and purification.

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.

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-).

Conservation of T cell epitopes between seasonal influenza viruses and the novel influenza A H7N9 virus

A novel avian influenza A(H7N9) virus recently emerged in the Yangtze River delta and caused diseases, often severe, in over 130 people. This H7N9 virus appeared to infect humans with greater ease than previous avian influenza virus subtypes such as H5N1 and H9N2. While there are other potential explanations for this large number of human infections with an avian influenza virus, we investigated whether a lack of conserved T-cell epitopes between endemic H1N1 and H3N2 influenza viruses and the novel H7N9 virus contributes to this observation. Here we demonstrate that a number of T cell epitopes are conserved between endemic H1N1 and H3N2 viruses and H7N9 virus. Most of these conserved epitopes are from viral internal proteins. The extent of conservation between endemic human seasonal influenza and avian influenza H7N9 was comparable to that with the highly pathogenic avian influenza H5N1. Thus, the ease of inter-species transmission of H7N9 viruses(compared with avian H5N1 viruses) cannot be attributed to the lack of conservation of such T cell epitopes. On the contrary, our findings predict significant T-cell based cross-reactions in the human population to the novel H7N9 virus. Our findings also have implications for H7N9 virus vaccine design.

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.

Prediction on Antigenic Epitope Characteristics of Bt Cry2Ab Protein in Transgenic Crops

[Objective] This study aimed to predict the structural characteristics of Bt Cry2Ab protein in transgenic crops with bioinformatic analysis to provide the theoretical clues for design of antibody Cry2Ab. [Method] The amino acid sequence of Cry2Ab protein was searched from NCBI database. The B cell epitopes were predicted with DNAStar. The binding affinity between Cry2Ab protein and MHC-II molecules was analyzed with NetMHCII 2.2 Server to predict the T cell epitopes. [Result] Prediction result suggested the potential B cell epitope of Cry2Ab locating in the region of 208-215. Analysis of the binding affinity between Cry2Ab and MHC-II molecules suggested the regions of 177-185, 299-307 and 255-263 were the potential T cell epitopes. Human with HLA-DRB10101 alleles and HLA-DRB10701 alleles were more sensitive to Cry2Ab protein. [Conclusion] This study facilitates to understand the structural characteristics of Cry2Ab protein and provides a new clue to improve the assessment method for potential allergenicity of genetically modified food.

Prediction of promiscuous T cell epitopes in RNA dependent RNA polymerase of Chikungunya virus

Objective: To explore RNA dependent RNA polymerase of Chikungunya virus(CHIKV) and develop T cell based epitopes with high antigenicity and good binding affinity for the human leukocyte antigen(HLA) classes as targets for epitopes based CHIKV vaccine. Methods: In this study we downloaded 371 non-structural protein 4 protein sequences of CHIKV belonging to different regions of the world from the US National Institute of Allergy and Infectious Diseases(NIAID) virus pathogen resource database. All the sequences were aligned by using CLUSTALW software and a consensus sequence was developed by using Uni Pro U Gene Software version 1.2.1. PropredⅠand Propred software were used to predict HLAⅠ and HLAⅡ binding promiscuous epitopes from the consensus sequence of non-structural protein 4 protein. The predicted epitopes were analyzed to determine their antigenicity through Vaxijen server version 2.0. All the HLAⅠ binding epitopes were scanned to determine their immunogenic potential through the Immune Epitope Database(IEDB). All the predicted epitopes of our study were fed to IEDB database to determine whether they had been tested earlier. Results: Twenty two HLA class Ⅱ epitopes and eight HLA classⅠepitopes were predicted. The promiscuous epitopes WMNMEVKII at position 486–494 and VRRLNAVLL at 331–339 were found to bind with 37 and 36 of the 51 HLA class Ⅱ alleles respectively. Epitope MANRSRYQS at position 58–66 and epitopes YQSRKVENM at positions 64–72 were predicted to bind with 12 and 9 HLAⅠI alleles with antigenicity scores of 0.754 9 and 1.013 0 respectively. Epitope YSPPINVRL was predicted to bind 18 HLAⅠ alleles and its antigenicity score was 1.425 9 and immunogenicity score was 0.173 83. This epitope is very useful in the preparation of a universal vaccine against CHIKV infection. Conclusions: Epitopes reported in this study showed promiscuity, antigenicity as well as good binding affinity for the HLA classes. These epitopes will provide the baseline for development of efficacious vaccine for CHIKV.

Prediction of promiscuous T-cell epitopes in the Zika virus polyprotein:An in silico approach

Objective:To predict immunogenic promiscuous T-cell epitopes from the polyprotein of the Zika virus using a range of bioinformatics tools.To date,no epitope data are available for the Zika virus in the IEDB database.Methods:We retrieved nearly 54 full length polyprotein sequences of the Zika virus from the NCBI database belonging to different outbreaks.A consensus sequence was then used to predict the promiscuous T cell epitopes that bind MHC 1 and MHC II alleles using Propred1 and Propred immunoinformatic algorithms respectively.The antigencity predicted score was also calculated for each predicted epitope using the Vaxi Jen 2.0 tool.Results:By using Pro Pred1,23 antigenic epitopes for HLA class I and 48 antigenic epitopes for HLA class II were predicted from the consensus polyprotein sequence of Zika virus.The greatest number of MHC class I binding epitopes were projected within the NS5(21%),followed by Envelope(17%).For MHC class II,greatest number of predicted epitopes were in NS5(19%) followed by the Envelope,NS1 and NS2(17% each).A variety of epitopes with good binding affinity,promiscuity and antigenicity were predicted for both the HLA classes.Conclusion:The predicted conserved promiscuous T-cell epitopes examined in this study were reported for the first time and will contribute to the imminent design of Zika virus vaccine candidates,which will be able to induce a broad range of immune responses in a heterogeneous HLA population.However,our results can be verified and employed in future efficacious vaccine formulations only after successful experimental studies.

Improving <i>in Silico</i>Prediction of Epitope Vaccine Candidates by Union and Intersection of Single Predictors

The in silico prediction of peptide binding affinities to MHC proteins is a very important first step in the process of epi-tope-based vaccine design and development. Five MHC class II binding prediction servers were combined in different ways and the resulting performance of these combinations was evaluated using a test set, which consisted of 4540 known HLA-DRB1 binders. The five servers were: NetMHCIIpan, NetMHCII, ProPred, RANKPEP, and EpiTOP. The top 5% of the ranked predictions from each server were combined using union and intersection operators. The outputs were evaluated in terms of sensitivity and positive predictive value (PPV). The union operator showed high sensitivity (65-79%) and low PPVs (6-8%), while intersection outputs had low sensitivities (4-41%) yet significantly higher PPVs (14-31%). Thus there is a defining trade-off between sensitivity and PPV for each combination. The union of outputs from different servers brings more “noise” than “signal” to the resulting set of predicted binders. Conversely, selecting only commonly predicted binders increases the probability that an identified binder is a true binder.

ITP患者PD-1/PD-L1表达特点及其在Treg与Breg细胞之间的相互作用机制分析

目的探讨原发免疫性血小板减少症(ITP)患者细胞程序性死亡受体-1(PD-1)/细胞程序性死亡配体1(PD-L1)表达特点及其在调节性T细胞(Treg)、调节性B细胞(Breg)间的相互作用。方法选取2018年12月—2022年1月在我院治疗的ITP患者106例作为观察组,其中轻度患者32例,中度患者44例,重度患者30例。同时选取同期健康志愿者100例作为对照组。检测两组Treg细胞百分比、Breg细胞百分比、Treg细胞表面PD-1阳性率、Breg细胞表面PD-L1阳性率等,同时分析观察组不同病情程度患者各指标差异。结果观察组Breg细胞百分比、Treg细胞百分比、TGF-β、IL-10和IL-4水平均明显低于对照组(P<0.05);观察组Treg细胞表面PD-1阳性率、Breg细胞表面PD-L1阳性率、可溶性程序性细胞死亡蛋白-1(sPD-1)和IL-17水平均明显高于对照组(均P<0.05);两组可溶性程序性细胞死亡蛋白配体-1(sPD-L1)水平比较差异无统计学意义(P>0.05)。观察组重度患者Breg细胞百分比、Treg细胞百分比均明显低于轻度和中度患者(均P<0.05),而Treg细胞表面PD-1阳性率、Breg细胞表面PD-L1阳性率均明显高于轻度和中度患者(均P<0.05)。Treg细胞表面PD-1阳性率与Breg细胞表面PD-L1阳性率呈正相关(r=0.446,P<0.05)。观察组治疗后Breg细胞百分比、Treg细胞百分比、TGF-β、IL-10和IL-4水平有所升高(P<0.05),而Treg细胞表面PD-1阳性率、Breg细胞表面PD-L1阳性率、sPD-1和IL-17水平有所降低(P<0.05),治疗前后sPD-L1水平比较差异无统计学意义(P>0.05)。结论ITP患者Treg细胞表面PD-1和Breg细胞表面PD-L1阳性率明显升高,与患者病情严重程度呈正相关,同时Treg细胞表面PD-1和Breg细胞表面PD-L1表达之间存在相关性。

BAFF调节免疫性血小板减少症模型小鼠的Th17/Treg平衡的研究

目的:探讨B细胞激活因子(BAFF)对免疫性血小板减少症模型小鼠体内辅助性T细胞17(Th17)/调节性T细胞(Treg)平衡的调节作用和潜在机制。方法:制备豚鼠抗小鼠血小板抗血清(GP-APS),并将150只无特定病原级别的成年雄性BALB/c小鼠(7~8周龄)随机分为5组,每组30只。分别为对照组(空白对照)和ITP组(GP-APS诱导),ITP+rhBAFF组(ITP组联合静脉注射50μg/kg/50μL重组人BAFF蛋白),并在ITP+rhBAFF组处理的基础上分别联合Notch1的抑制剂(DAPT)或PI3K/Akt的抑制剂Polygalacin D(PGD),设立ITP+rhBAFF+DAPT组和ITP+rhBAFF+PGD组,除对照组和ITP组外,均为静脉注射给药,DAPT注射剂量100μg/kg;PGD注射剂量25μg/kg,静脉注射总体积均为50μL,每日1次。1周后取小鼠1mL外周血并分离血清和单个核细胞。用免疫荧光化学检测单个核细胞中BAFF和Notch1的定位。对外周血中的血小板进行计数。酶联免疫吸附法(ELSIA)检测小鼠外周血血清BAFF的水平。Western blot检测小鼠外周血单个核细胞中PI3K、AKT、Notch1、p-Akt(Thr308)、p-Akt(Ser473)的蛋白表达。流式细胞术检测单个核细胞中Th17/Treg的比例变化。结果:ITP小鼠外周血单个核细胞的BAFF与Notch1共定位在细胞膜。与对照组比较,ITP组BAFF、Notch1、p-Akt(Thr308)、p-Akt(Ser473)的表达增加,血小板数目和Treg比例减少,Th17比例增加(P<0.05)。与ITP组比较,ITP+rhBAFF组BAFF、Notch1、p-Akt(Thr308)、p-Akt(Ser473)的表达增加,血小板数目和Treg比例减少,Th17比例增加(P<0.05)。与ITP+rhBAFF组比较,ITP+rhBAFF+DAPT组BAFF、Notch1、p-Akt(Thr308)、p-Akt(Ser473)的表达降低,血小板数目和Treg比例增加,Th17比例降低(P<0.05)。与ITP+rhBAFF组比较,ITP+rhBAFF+PGD组BAFF、Notch1、p-Akt(Thr308)、p-Akt(Ser473)的表达降低,血小板数目和Treg比例增加,Th17比例降低(P<0.05)。结论:BAFF通过激活Notch1/PI3K/Akt信号通路促进免疫性血小板减少症模型小鼠体内Th17比例增加及Treg比例减少。

淋巴结滤泡辅助T细胞淋巴瘤伴B细胞克隆性增生10例临床病理特征分析

目的探讨淋巴结滤泡辅助T细胞淋巴瘤血管免疫母细胞型(nodal follicular helper T cell lymphoma,angioimmunoblastic-type,nTFHL-AI)伴B细胞克隆性增生的临床病理学特征、免疫表型、分子特征、治疗及预后。方法收集10例nTFHL-AI伴B细胞克隆性增生患者的临床病理资料,分别行HE、免疫组化和基因重排检测,并复习相关文献。结果10例患者中男性5例,女性5例,中位年龄73岁。临床表现以全身淋巴结肿大、脾肿大及B症状为主;Ann Arbor分期:Ⅳ期8例,Ⅰ+Ⅱ期2例。实验室检查以β2微球蛋白和乳酸脱氢酶(LDH)升高,血红蛋白、红细胞和血小板减少为主,血浆EBV核酸定量阳性8例。镜下均可见典型结节状聚集或散在的透明细胞、分枝状高内皮血管及增生杂乱“风吹”状的滤泡树突网。肿瘤细胞背景中嗜酸性粒细胞浸润0~5个/HPF 7例,5~10个/HPF 2例,>50个/HPF 1例。浆细胞含量≤5%6例,浆细胞含量10%和20%各1例,浆细胞含量较多(30%)2例。组织细胞明显增生7例。见RS样大细胞1例。背景中含大量B细胞5例,含少量B细胞5例。10例患者均表达T细胞标志物,滤泡辅助性T细胞标志物CD10、BCL6、CXCL13和PD-1同时阳性6例,BCL6、CXCL13和PD-1同时阳性10例。EBER原位杂交阳性8例。10例患者均检测到TCR基因重排和IG基因重排阳性。所有患者诊断后均行化疗,其中3例疾病进展死亡。结论伴B细胞克隆性增生nTFHL-AI中,B细胞的克隆性增生与EBV是否感染及感染细胞的数量无关,同时浆细胞增生提示预后不良。

慢性HBV感染者外周血可诱导共刺激分子在CD8+ T淋巴细胞的表达及其临床意义

目的 探讨慢性乙型肝炎病毒(HBV)感染者外周血可诱导共刺激分子(ICOS)在CD8+T淋巴细胞的表达特点及临床意义。方法 选取2017年5月—2018年10月就诊的慢性乙型肝炎(CHB)100例、HBV-肝硬化(LC)25例和HBV-慢加急(或亚急)性肝衰竭(ACLF)26例分别纳入CHB组、HBV-LC组和HBV-ACLF组,健康对照(NC)组35例来自同期门诊体检健康者。采用流式细胞仪检测各组ICOS在CD8+T淋巴细胞的表达情况;分析CD8+T淋巴细胞ICOS表达水平与慢性HBV感染者疾病严重程度、HBV-ACLF预后及并发症的相关性;动态观察HBV-ACLF患者治疗过程中CD8+T淋巴细胞ICOS表达变化。结果 HBV-ACLF组外周血CD8+T淋巴细胞ICOS表达比率及平均荧光强度(MFI)均高于CHB组、HBV-LC组和NC组(P<0.05)。慢性HBV感染者ICOS的MFI与白蛋白、胆碱酯酶、总胆固醇、血红蛋白呈负相关(r=-0.263、-0.269、-0.273、-0.302,P=0.003、0.003、0.011、0.004);与直接胆红素、天冬氨酸转氨酶、凝血酶原时间、国际标准化比值呈正相关(r=0.248、0.208、0.331、0.315,P=0.005、0.020、0.003、0.009);与HBV-DNA、腹水及感染无明显相关性(P>0.05)。治疗过程中,HBV-ACLF患者ICOS的MFI无明显改变。但生存组ICOS的MFI在治疗第1周时较治疗前上升(P<0.05)。结论 HBV-ACLF患者外周血CD8+T淋巴细胞ICOS的表达水平明显升高,并与肝脏合成功能、炎症程度及预后相关,治疗早期ICOS水平变化有助于预测慢性HBV感染者的预后。

儿童CD19 CAR-T细胞治疗相关B细胞再生障碍的临床意义和对策

急性B系淋巴细胞白血病(B-ALL)患儿在CD 19 CAR-T细胞治疗后普遍发生B细胞再生障碍(BCA),BCA持续的时间长短对患者的免疫状态及预后会产生影响。对BCA的充分认识有助于临床医师科学、规范、合理地选择治疗策略,减少CAR-T治疗后白血病患儿的感染机会,提高生活质量,改善预后。

伴单克隆B淋巴细胞和单克隆浆细胞增殖的AITL 1例

血管免疫母细胞性T细胞淋巴瘤(angioimmunoblastic T-cell lymphoma,AITL)是一种预后较差的侵袭性淋巴瘤。本文报道1例伴单克隆B淋巴细胞和单克隆浆细胞增殖AITL患者的诊疗经过,以提高对AITL的认识及诊疗水平,从而减少漏诊和误诊。

非洲猪瘟病毒T、B细胞表位的免疫信息学预测与分析

旨在通过免疫信息学方法预测非洲猪瘟病毒(ASFV)结构蛋白的T、B细胞表位,为非洲猪瘟(ASF)表位疫苗的设计研制提供参考。从NCBI和RCSB数据库获取ASFV蛋白质序列和三维结构,利用IEDB、DTU Health Tech等数据库的生物信息学工具对ASFV的5种结构蛋白p72、p17、p49、M1249L和H240R的细胞毒性T细胞表位、线性B细胞和构象B细胞表位进行鉴定。结果显示:5种蛋白质均为亲水性,二级结构以无规则卷曲为主,仅M1249L例外;预测到抗原性良好、无毒、无致敏的细胞毒性T细胞优势表位27个,线性B细胞优势表位35个;预测到仅针对p72的构象B细胞优势表位2个。结论:ASFV的5种蛋白质可能具有多个潜在T、B细胞表位,其中B细胞表位相对占优,5种蛋白质中p72和M1249L最具疫苗研发前景,可结合蛋白质相关参数信息为构建ASF表位疫苗提供参考。