基于多亚单位Th表位的幽门螺杆菌疫苗的研究
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摘要
幽门螺杆菌(Helicobacter pylori, H. pylori)在全球人口中的感染率超过50%，已被确定为慢性胃炎、消化性溃疡的重要致病菌，并被世界卫生组织列为胃癌的Ⅰ类致癌因子。
表位是抗原分子中决定抗原特异性的关键部分，合理组合优势表位，可诱导出比原始抗原更为高效和特异的免疫应答。H. pylori感染导致机体对H. pylori自身天然抗原产生免疫耐受，选择H. pylori保护性抗原的优势表位来构建表位疫苗，有可能打破免疫耐受，从而达到免疫预防和清除H. pylori感染的目的。前期研究证实，特异性CD4+T细胞应答在抗H. pylori感染的保护性免疫应答中至关重要。本研究通过构建H. pylori Th表位疫苗，采用先免疫后攻毒以及先感染后治疗两种方式，在动物模型上对疫苗的预防和清除的保护效果进行评价，并探讨相应的免疫应答机制。主要研究方法、结果和结论如下：
1.幽门螺杆菌Th表位的筛选和疫苗的设计
通过生物信息学的方法预测并筛选H. pylori保护性抗原HpaA、CagA和UreB的优势Th表位，共筛选到17个表位肽。动力学模拟考察不同表位连接顺序所构成蛋白的动力学和热力学稳定型，确定以HpaA表位-CagA表位-UreB表位的连接顺序来构建Th表位疫苗Epivac。
2.幽门螺杆菌Th表位疫苗的构建、表达和纯化
构建疫苗蛋白的原核表达质粒pET30a-epivac，转化至BL21(DE3)，经诱导表达和纯化，获得目的蛋白Epivac，HPLC分析蛋白纯度在90%以上。相同的技术方法制备含分子内佐剂的疫苗蛋白LTB-epivac。
3.幽门螺杆菌Th表位疫苗的免疫保护效果评价及应答分析
1)幽门螺杆菌Th表位疫苗免疫预防效果的评价及应答分析
采用鼻腔滴注和皮下注射两种免疫途径，Epivac联用不同佐剂对BALB/c小鼠进行免疫，评价疫苗的免疫预防效果。结果显示，单用疫苗以及联用佐剂都可以有效预防H. pylori感染，且联用佐剂效果更优。此外，鼻腔滴注发挥保护作用的时间点要早于皮下注射。ELISA检测特异性抗体IgG、IgA的产生；Real-time RT PCR和ELISA检测脾淋巴细胞和胃组织细胞因子的表达变化；流式细胞术定量检测抗原特异性CD4+T细胞的水平及其应答特征。结果提示疫苗的保护作用与抗体应答无关，而主要依赖于疫苗诱导的系统性和局部的Th1型CD4+T细胞应答。
2)幽门螺杆菌Th表位疫苗免疫清除效果的评价及应答分析：
利用BALB/c小鼠模型对表位疫苗的免疫清除效果进行评价。相对于未免疫组，疫苗免疫可以显著降低小鼠胃内H. pylori的定植量，具有一定的治疗效果。通过分析小鼠抗体应答的特征，推测疫苗的免疫清除作用可能与特异性Th1型细胞应答密切相关。
4.幽门螺杆菌Th表位疫苗的初步安全性评价
通过内毒素检测、急性毒性试验和豚鼠最大化试验对疫苗的安全性进行初步评价，结果显示疫苗内毒素低于限量，且鼻腔滴注和皮下注射两种给药方式不会引起机体损伤和过敏反应，初步说明疫苗是安全无毒的。
Helicobacter pylori (H. pylori) is a common bacterium, and approximately50percentof the world's population has been estimated to be infected. H. pylori infection is a keyetiological factor in chronic gastritis, peptic ulcer disease, and was listed as a class Icarcinogen by World Health Organization (WHO).
Antigens are known to display their specificity mainly through epitopes. Consisting ofepitopes from versatile antigens, epitope-based vaccines are capable of inducing morespecific and potent immune responses than whole antigens. H. pylori infection leads to thebody's immunological tolerance to natural antigen. Rational combination ofimmunodominant epitopes selected from protective antigens is possible to break theimmune tolerance, so as to confer protection against H. pylori infection. Previous studiesindicates that specific CD4+T cell response is critical to the protective immunity. In thisstudy, we constructed a H. pylori Th epitope-based vaccine, and the prophylactic andtherapeutic potential was examined. Research methods, results and conclusions are asfollows:
1. H. pylori Th epitopes screen and vaccine design
By means of bioinformatic algorithms, potential immunodominant CD4+T cellepitopes were screened from HpaA, UreB and CagA genes. Kinetic and thermodynamicstability of the various combinations of epitopes was analyzed by dynamics simulation, andthe theoretic optimal combination was HpaAepi-CagAepi-UreBepi.
2. Construction, expression and purification of the vaccine
Synthetic oligonucleotides encoding Epivac were ligated into the XhoⅠ-NdeⅠ sitesof the pET30a vector. Then the recombinant plasmid was transformed into E.coliBL21(DE3). After induction and purification, Epivac was obtained and was more than90%pure as determined by HPLC. LTB-epivac was obtained by the same method.
3. Evaluation of protective effect of the vaccine and underlying mechanisms
In the presence of several different adjuvants, BALB/c mice were intranasally and subcutaneously immunized with Epivac and subsequently challenged with H. pylori. Theprotective effect was achieved4weeks post challenge. The results show Epivac alone orwith an adjuvant significantly reduced H. pylori colonization and better protection wasobserved when an adjuvant was used. In addition, the protective effect was observed earlierwhen immunized intranasally. Epivac-specific IgG, IgG1, IgG2a and sIgA were measuredby ELISA, and systemic and gastric cytokine expression was also measured by Real-timeRT-PCR and ELISA. Quantitation and characterization of Epivac-specific CD4+T cellswere determined by flow cytometry. Epivac-mediated protective immunity against H. pyloriinfection may occur by antibody-independent mechanisms, and Epivac-mediated local andsystemic Th1-biased immune response may contribute to the protective immunity.
4. Evaluation of therapeutic effect of the vaccine and underlying mechanisms
Therapeutic effect of the vaccine was evaluated by BALB/c mice. Compared tonon-immunized mice, immunization with Epivac alone or with an adjuvant significantlyreduced H. pylori colonization. By analysis of the characteristics of the antibody response inmice, we concluded that the Th1-biased response may correlate with the eradication of H.pylori.
5. Safety evaluation of the vaccine
The endotoxin level of the vaccine was determined by endotoxin measure kit, andAcute Toxicity Test (ATT) and Guinea pig maximization test (GPMT) was used to evaluatethe safety of the vaccine. Results showed that endotoxin level is below the limit, andintranasally and subcutaneously immunization would not cause body injury and skinsensitization. This study indicates that the vaccine is safe and non-toxic.
表位是抗原分子中决定抗原特异性的关键部分，合理组合优势表位，可诱导出比原始抗原更为高效和特异的免疫应答。H. pylori感染导致机体对H. pylori自身天然抗原产生免疫耐受，选择H. pylori保护性抗原的优势表位来构建表位疫苗，有可能打破免疫耐受，从而达到免疫预防和清除H. pylori感染的目的。前期研究证实，特异性CD4+T细胞应答在抗H. pylori感染的保护性免疫应答中至关重要。本研究通过构建H. pylori Th表位疫苗，采用先免疫后攻毒以及先感染后治疗两种方式，在动物模型上对疫苗的预防和清除的保护效果进行评价，并探讨相应的免疫应答机制。主要研究方法、结果和结论如下：
1.幽门螺杆菌Th表位的筛选和疫苗的设计
通过生物信息学的方法预测并筛选H. pylori保护性抗原HpaA、CagA和UreB的优势Th表位，共筛选到17个表位肽。动力学模拟考察不同表位连接顺序所构成蛋白的动力学和热力学稳定型，确定以HpaA表位-CagA表位-UreB表位的连接顺序来构建Th表位疫苗Epivac。
2.幽门螺杆菌Th表位疫苗的构建、表达和纯化
构建疫苗蛋白的原核表达质粒pET30a-epivac，转化至BL21(DE3)，经诱导表达和纯化，获得目的蛋白Epivac，HPLC分析蛋白纯度在90%以上。相同的技术方法制备含分子内佐剂的疫苗蛋白LTB-epivac。
3.幽门螺杆菌Th表位疫苗的免疫保护效果评价及应答分析
1)幽门螺杆菌Th表位疫苗免疫预防效果的评价及应答分析
采用鼻腔滴注和皮下注射两种免疫途径，Epivac联用不同佐剂对BALB/c小鼠进行免疫，评价疫苗的免疫预防效果。结果显示，单用疫苗以及联用佐剂都可以有效预防H. pylori感染，且联用佐剂效果更优。此外，鼻腔滴注发挥保护作用的时间点要早于皮下注射。ELISA检测特异性抗体IgG、IgA的产生；Real-time RT PCR和ELISA检测脾淋巴细胞和胃组织细胞因子的表达变化；流式细胞术定量检测抗原特异性CD4+T细胞的水平及其应答特征。结果提示疫苗的保护作用与抗体应答无关，而主要依赖于疫苗诱导的系统性和局部的Th1型CD4+T细胞应答。
2)幽门螺杆菌Th表位疫苗免疫清除效果的评价及应答分析：
利用BALB/c小鼠模型对表位疫苗的免疫清除效果进行评价。相对于未免疫组，疫苗免疫可以显著降低小鼠胃内H. pylori的定植量，具有一定的治疗效果。通过分析小鼠抗体应答的特征，推测疫苗的免疫清除作用可能与特异性Th1型细胞应答密切相关。
4.幽门螺杆菌Th表位疫苗的初步安全性评价
通过内毒素检测、急性毒性试验和豚鼠最大化试验对疫苗的安全性进行初步评价，结果显示疫苗内毒素低于限量，且鼻腔滴注和皮下注射两种给药方式不会引起机体损伤和过敏反应，初步说明疫苗是安全无毒的。
Helicobacter pylori (H. pylori) is a common bacterium, and approximately50percentof the world's population has been estimated to be infected. H. pylori infection is a keyetiological factor in chronic gastritis, peptic ulcer disease, and was listed as a class Icarcinogen by World Health Organization (WHO).
Antigens are known to display their specificity mainly through epitopes. Consisting ofepitopes from versatile antigens, epitope-based vaccines are capable of inducing morespecific and potent immune responses than whole antigens. H. pylori infection leads to thebody's immunological tolerance to natural antigen. Rational combination ofimmunodominant epitopes selected from protective antigens is possible to break theimmune tolerance, so as to confer protection against H. pylori infection. Previous studiesindicates that specific CD4+T cell response is critical to the protective immunity. In thisstudy, we constructed a H. pylori Th epitope-based vaccine, and the prophylactic andtherapeutic potential was examined. Research methods, results and conclusions are asfollows:
1. H. pylori Th epitopes screen and vaccine design
By means of bioinformatic algorithms, potential immunodominant CD4+T cellepitopes were screened from HpaA, UreB and CagA genes. Kinetic and thermodynamicstability of the various combinations of epitopes was analyzed by dynamics simulation, andthe theoretic optimal combination was HpaAepi-CagAepi-UreBepi.
2. Construction, expression and purification of the vaccine
Synthetic oligonucleotides encoding Epivac were ligated into the XhoⅠ-NdeⅠ sitesof the pET30a vector. Then the recombinant plasmid was transformed into E.coliBL21(DE3). After induction and purification, Epivac was obtained and was more than90%pure as determined by HPLC. LTB-epivac was obtained by the same method.
3. Evaluation of protective effect of the vaccine and underlying mechanisms
In the presence of several different adjuvants, BALB/c mice were intranasally and subcutaneously immunized with Epivac and subsequently challenged with H. pylori. Theprotective effect was achieved4weeks post challenge. The results show Epivac alone orwith an adjuvant significantly reduced H. pylori colonization and better protection wasobserved when an adjuvant was used. In addition, the protective effect was observed earlierwhen immunized intranasally. Epivac-specific IgG, IgG1, IgG2a and sIgA were measuredby ELISA, and systemic and gastric cytokine expression was also measured by Real-timeRT-PCR and ELISA. Quantitation and characterization of Epivac-specific CD4+T cellswere determined by flow cytometry. Epivac-mediated protective immunity against H. pyloriinfection may occur by antibody-independent mechanisms, and Epivac-mediated local andsystemic Th1-biased immune response may contribute to the protective immunity.
4. Evaluation of therapeutic effect of the vaccine and underlying mechanisms
Therapeutic effect of the vaccine was evaluated by BALB/c mice. Compared tonon-immunized mice, immunization with Epivac alone or with an adjuvant significantlyreduced H. pylori colonization. By analysis of the characteristics of the antibody response inmice, we concluded that the Th1-biased response may correlate with the eradication of H.pylori.
5. Safety evaluation of the vaccine
The endotoxin level of the vaccine was determined by endotoxin measure kit, andAcute Toxicity Test (ATT) and Guinea pig maximization test (GPMT) was used to evaluatethe safety of the vaccine. Results showed that endotoxin level is below the limit, andintranasally and subcutaneously immunization would not cause body injury and skinsensitization. This study indicates that the vaccine is safe and non-toxic.
引文
[1] NIH Consensus Conference. Helicobacter pylori in peptic ulcer disease. NIHConsensus Development Panel on Helicobacter pylori in Peptic Ulcer Disease. JAMA1994;272(1):65-9.
[2] Peek RM, Jr., Crabtree JE. Helicobacter infection and gastric neoplasia. J Pathol2006;208(2):233-48.
[3] Chiba N, Rao BV, Rademaker JW, Hunt RH. Meta-analysis of the efficacy of antibiotictherapy in eradicating Helicobacter pylori. Am J Gastroenterol1992;87(12):1716-27.
[4] Graham DY, Fischbach L. Helicobacter pylori treatment in the era of increasingantibiotic resistance. Gut2010;59(8):1143-53.
[5] Hojsak I, Kos T, Dumancic J, Misak Z, Jadresin O, Jaklin Kekez A, et al. Antibioticresistance of Helicobacter pylori in pediatric patients--10years' experience. Eur JPediatr2012;171(9):1325-30.
[6] Lionetti E, Indrio F, Pavone L, Borrelli G, Cavallo L, Francavilla R. Role of probioticsin pediatric patients with Helicobacter pylori infection: a comprehensive review of theliterature. Helicobacter2010;15(2):79-87.
[7] Franceschi F, Cazzato A, Nista EC, Scarpellini E, Roccarina D, Gigante G, et al. Roleof probiotics in patients with Helicobacter pylori infection. Helicobacter2007;12Suppl2:59-63.
[8] Rupnow MF, Chang AH, Shachter RD, Owens DK, Parsonnet J. Cost-effectiveness ofa potential prophylactic Helicobacter pylori vaccine in the United States. J Infect Dis2009;200(8):1311-7.
[9] Czinn SJ, Blanchard T. Vaccinating against Helicobacter pylori infection. Nat RevGastroenterol Hepatol2011;8(3):133-40.
[10] Del Giudice G, Malfertheiner P, Rappuoli R. Development of vaccines againstHelicobacter pylori. Expert Rev Vaccines2009;8(8):1037-49.
[11] Liu KY, Shi Y, Luo P, Yu S, Chen L, Zhao Z, et al. Therapeutic efficacy of oralimmunization with attenuated Salmonella typhimurium expressing Helicobacter pyloriCagA, VacA and UreB fusion proteins in mice model. Vaccine2011;29(38):6679-85.
[12] DiPetrillo MD, Tibbetts T, Kleanthous H, Killeen KP, Hohmann EL. Safety andimmunogenicity of phoP/phoQ-deleted Salmonella typhi expressing Helicobacterpylori urease in adult volunteers. Vaccine1999;18(5-6):449-59.
[13] Metzger WG, Mansouri E, Kronawitter M, Diescher S, Soerensen M, Hurwitz R, et al.Impact of vector-priming on the immunogenicity of a live recombinant Salmonellaenterica serovar typhi Ty21a vaccine expressing urease A and B from Helicobacterpylori in human volunteers. Vaccine2004;22(17-18):2273-7.
[14] Marchetti M, Rossi M, Giannelli V, Giuliani MM, Pizza M, Censini S, et al. Protectionagainst Helicobacter pylori infection in mice by intragastric vaccination with H. pyloriantigens is achieved using a non-toxic mutant of E. coli heat-labile enterotoxin (LT) asadjuvant. Vaccine1998;16(1):33-7.
[15] Smythies LE, Novak MJ, Waites KB, Lindsey JR, Morrow CD, Smith PD. Poliovirusreplicons encoding the B subunit of Helicobacter pylori urease protect mice against H.pylori infection. Vaccine2005;23(7):901-9.
[16] Corthesy B, Boris S, Isler P, Grangette C, Mercenier A. Oral immunization of micewith lactic acid bacteria producing Helicobacter pylori urease B subunit partiallyprotects against challenge with Helicobacter felis. J Infect Dis2005;192(8):1441-9.
[17] Wu C, Shi Y, Guo H, Zou WY, Guo G, Xie QH, et al. Protection against Helicobacterpylori infection in mongolian gerbil by intragastric or intramuscular administration ofH. pylori multicomponent vaccine. Helicobacter2008;13(3):191-9.
[18] Zhang L, Yang Y, Yang X, Zhao J, Yang J, Liu F, et al. T cell epitope-basedpeptide-DNA dual vaccine induces protective immunity against Schistosomajaponicum infection in C57BL/6J mice. Microbes Infect2008;10(3):251-9.
[19] Sette A, Fikes J. Epitope-based vaccines: an update on epitope identification, vaccinedesign and delivery. Curr Opin Immunol2003;15(4):461-70.
[20] Goldstein G, Chicca JJ,2nd. A universal anti-HIV-1Tat epitope vaccine that is fullysynthetic and self-adjuvanting. Vaccine2010;28(4):1008-14.
[21] Ahlers JD, Belyakov IM. Lessons learned from natural infection: focusing on thedesign of protective T cell vaccines for HIV/AIDS. Trends Immunol2010;31(3):120-30.
[22] Ingram RJ, Metan G, Maillere B, Doganay M, Ozkul Y, Kim LU, et al. Naturalexposure to cutaneous anthrax gives long-lasting T cell immunity encompassinginfection-specific epitopes. J Immunol2010;184(7):3814-21.
[23] Jin X, Newman MJ, De-Rosa S, Cooper C, Thomas E, Keefer M, et al. A novel HIV Thelper epitope-based vaccine elicits cytokine-secreting HIV-specific CD4+T cells in aPhase I clinical trial in HIV-uninfected adults. Vaccine2009;27(50):7080-6.
[24] Paul S, Planque S, Nishiyama Y, Escobar M, Hanson C. Back to the future: covalentepitope-based HIV vaccine development. Expert Rev Vaccines2010;9(9):1027-43.
[25] Gupta SK, Smita S, Sarangi AN, Srivastava M, Akhoon BA, Rahman Q. In silicoCD4+T-cell epitope prediction and HLA distribution analysis for the potential proteinsof Neisseria meningitidis Serogroup B--a clue for vaccine development. Vaccine2010;28(43):7092-7.
[26] McNamara LA, He Y, Yang Z. Using epitope predictions to evaluate efficacy andpopulation coverage of the Mtb72f vaccine for tuberculosis. BMC Immunol2010;11:18.
[27] Zhou WY, Shi Y, Wu C, Zhang WJ, Mao XH, Guo G, et al. Therapeutic efficacy of amulti-epitope vaccine against Helicobacter pylori infection in BALB/c mice model.Vaccine2009;27(36):5013-9.
[28][28] Moss SF, Moise L, Lee DS, Kim W, Zhang S, Lee J, et al. HelicoVax:epitope-based therapeutic Helicobacter pylori vaccination in a mouse model. Vaccine2011;29(11):2085-91.
[29] Flach CF, Svensson N, Blomquist M, Ekman A, Raghavan S, Holmgren J. A truncatedform of HpaA is a promising antigen for use in a vaccine against Helicobacter pylori.Vaccine2011;29(6):1235-41.
[30] Sutton P, Doidge C, Pinczower G, Wilson J, Harbour S, Swierczak A, et al.Effectiveness of vaccination with recombinant HpaA from Helicobacter pylori isinfluenced by host genetic background. FEMS Immunol Med Microbiol2007;50(2):213-9.
[31] Zhang H, Liu M, Li Y, Zhao Y, He H, Yang G, et al. Oral immunogenicity andprotective efficacy in mice of a carrot-derived vaccine candidate expressing UreBsubunit against Helicobacter pylori. Protein Expr Purif2010;69(2):127-31.
[32] Lee MH, Roussel Y, Wilks M, Tabaqchali S. Expression of Helicobacter pylori ureasesubunit B gene in Lactococcus lactis MG1363and its use as a vaccine delivery systemagainst H. pylori infection in mice. Vaccine2001;19(28-29):3927-35.
[33] Rossi G, Ruggiero P, Peppoloni S, Pancotto L, Fortuna D, Lauretti L, et al. Therapeuticvaccination against Helicobacter pylori in the beagle dog experimental model: safety,immunogenicity, and efficacy. Infect Immun2004;72(6):3252-9.
[34] Sayi A, Kohler E, Hitzler I, Arnold I, Schwendener R, Rehrauer H, et al. The CD4+Tcell-mediated IFN-gamma response to Helicobacter infection is essential for clearanceand determines gastric cancer risk. J Immunol2009;182(11):7085-101.
[35] Ermak TH, Giannasca PJ, Nichols R, Myers GA, Nedrud J, Weltzin R, et al.Immunization of mice with urease vaccine affords protection against Helicobacterpylori infection in the absence of antibodies and is mediated by MHC class II-restrictedresponses. J Exp Med1998;188(12):2277-88.
[36] Allison CC, Ferrero RL. Role of virulence factors and host cell signaling in therecognition of Helicobacter pylori and the generation of immune responses. FutureMicrobiol2010;5(8):1233-55.
[37] Prinz C, Hafsi N, Voland P. Helicobacter pylori virulence factors and the host immuneresponse: implications for therapeutic vaccination. Trends Microbiol2003;11(3):134-8.
[38] Kim Y, Sette A, Peters B. Applications for T-cell epitope queries and tools in theImmune Epitope Database and Analysis Resource. J Immunol Methods2011;374(1-2):62-9.
[39] Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, et al. Immuneepitope database analysis resource. Nucleic Acids Res2012;40(Web Serverissue):W525-30.
[40] Iankov ID, Haralambieva IH, Galanis E. Immunogenicity of attenuated measles virusengineered to express Helicobacter pylori neutrophil-activating protein. Vaccine2011;29(8):1710-20.
[41] Craiu A, Gaczynska M, Akopian T, Gramm CF, Fenteany G, Goldberg AL, et al.Lactacystin and clasto-lactacystin beta-lactone modify multiple proteasomebeta-subunits and inhibit intracellular protein degradation and major histocompatibilitycomplex class I antigen presentation. J Biol Chem1997;272(20):13437-45.
[42] Cunningham BC, Wells JA. High-resolution epitope mapping of hGH-receptorinteractions by alanine-scanning mutagenesis. Science1989;244(4908):1081-5.
[43] Schofield DJ, Pope AR, Clementel V, Buckell J, Chapple S, Clarke KF, et al.Application of phage display to high throughput antibody generation andcharacterization. Genome Biol2007;8(11):R254.
[44] Fridman A, Finnefrock AC, Peruzzi D, Pak I, La Monica N, Bagchi A, et al. Anefficient T-cell epitope discovery strategy using in silico prediction and the iTopiaassay platform. Oncoimmunology2012;1(8):1258-70.
[45] Bernardeau K, Kerzhero J, Fortun A, Moreau-Aubry A, Favry E, Echasserieau K, et al.A simple competitive assay to determine peptide affinity for HLA class II molecules: auseful tool for epitope prediction. J Immunol Methods2011;371(1-2):97-105.
[46] Sabarth N, Hurwitz R, Meyer TF, Bumann D. Multiparameter selection of Helicobacterpylori antigens identifies two novel antigens with high protective efficacy. InfectImmun2002;70(11):6499-503.
[47] Charoentong P, Angelova M, Efremova M, Gallasch R, Hackl H, Galon J, et al.Bioinformatics for cancer immunology and immunotherapy. Cancer ImmunolImmunother2012;61(11):1885-903.
[48] Batori V, Friis EP, Nielsen H, Roggen EL. An in silico method using an epitope motifdatabase for predicting the location of antigenic determinants on proteins in a structuralcontext. J Mol Recognit2006;19(1):21-9.
[49] Bhasin M, Raghava GP. Prediction of CTL epitopes using QM, SVM and ANNtechniques. Vaccine2004;22(23-24):3195-204.
[50] Vider-Shalit T, Louzoun Y. MHC-I prediction using a combination of T cell epitopesand MHC-I binding peptides. J Immunol Methods2011;374(1-2):43-6.
[51] Ravindra R, Zhao S, Gies H, Winter R. Protein encapsulation in mesoporous silicate:the effects of confinement on protein stability, hydration, and volumetric properties. JAm Chem Soc2004;126(39):12224-5.
[52] Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalablemolecular dynamics with NAMD. J Comput Chem2005;26(16):1781-802.
[53] Wang Y, Harrison CB, Schulten K, McCammon JA. Implementation of AcceleratedMolecular Dynamics in NAMD. Comput Sci Discov2011;4(1).
[54] Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph1996;14(1):33-8,27-8.
[55] Zhuang Z, Peng Q, Li Y. Controlled synthesis of semiconductor nanostructures in theliquid phase. Chem Soc Rev2011;40(11):5492-513.
[56] Friligou I, Papadimitriou E, Gatos D, Matsoukas J, Tselios T. Microwave-assistedsolid-phase peptide synthesis of the60-110domain of human pleiotrophin on2-chlorotrityl resin. Amino Acids2011;40(5):1431-40.
[57] Pattabiraman VR, Ogunkoya AO, Bode JW. Chemical Protein Synthesis byChemoselective alpha-Ketoacid-Hydroxylamine (KAHA) Ligations with5-Oxaproline.Angew Chem Int Ed Engl2012.
[58] Hunt I. From gene to protein: a review of new and enabling technologies formulti-parallel protein expression. Protein Expr Purif2005;40(1):1-22.
[59] Li J, Menzel C, Meier D, Zhang C, Dubel S, Jostock T. A comparative study ofdifferent vector designs for the mammalian expression of recombinant IgG antibodies.J Immunol Methods2007;318(1-2):113-24.
[60] Sorensen HP, Mortensen KK. Advanced genetic strategies for recombinant proteinexpression in Escherichia coli. J Biotechnol2005;115(2):113-28.
[61] Ventura S, Villaverde A. Protein quality in bacterial inclusion bodies. TrendsBiotechnol2006;24(4):179-85.
[62][62] Weiner AJ, Geysen HM, Christopherson C, Hall JE, Mason TJ, Saracco G, et al.Evidence for immune selection of hepatitis C virus (HCV) putative envelopeglycoprotein variants: potential role in chronic HCV infections. Proc Natl Acad Sci US A1992;89(8):3468-72.
[63] Calvo-Calle JM, Oliveira GA, Watta CO, Soverow J, Parra-Lopez C, Nardin EH. Alinear peptide containing minimal T-and B-cell epitopes of Plasmodium falciparumcircumsporozoite protein elicits protection against transgenic sporozoite challenge.Infect Immun2006;74(12):6929-39.
[64] Singh SM, Panda AK. Solubilization and refolding of bacterial inclusion body proteins.J Biosci Bioeng2005;99(4):303-10.
[65] Lilie H, Schwarz E, Rudolph R. Advances in refolding of proteins produced in E. coli.Curr Opin Biotechnol1998;9(5):497-501.
[66] Tsumoto K, Ejima D, Kumagai I, Arakawa T. Practical considerations in refoldingproteins from inclusion bodies. Protein Expr Purif2003;28(1):1-8.
[67] Kramberger P, Peterka M, Boben J, Ravnikar M, Strancar A. Short monolithiccolumns--a breakthrough in purification and fast quantification of tomato mosaic virus.J Chromatogr A2007;1144(1):143-9.
[68] Lehmberg E, Traina JA, Chakel JA, Chang RJ, Parkman M, McCaman MT, et al.Reversed-phase high-performance liquid chromatographic assay for the adenovirustype5proteome. J Chromatogr B Biomed Sci Appl1999;732(2):411-23.
[69] Eisenberg JC, Czinn SJ, Garhart CA, Redline RW, Bartholomae WC, Gottwein JM, etal. Protective efficacy of anti-Helicobacter pylori immunity following systemicimmunization of neonatal mice. Infect Immun2003;71(4):1820-7.
[70] Gottwein JM, Blanchard TG, Targoni OS, Eisenberg JC, Zagorski BM, Redline RW, etal. Protective anti-Helicobacter immunity is induced with aluminum hydroxide orcomplete Freund's adjuvant by systemic immunization. J Infect Dis2001;184(3):308-14.
[71] Guy B, Hessler C, Fourage S, Haensler J, Vialon-Lafay E, Rokbi B, et al. Systemicimmunization with urease protects mice against Helicobacter pylori infection. Vaccine1998;16(8):850-6.
[72] Douce G, Turcotte C, Cropley I, Roberts M, Pizza M, Domenghini M, et al. Mutants ofEscherichia coli heat-labile toxin lacking ADP-ribosyltransferase activity act asnontoxic, mucosal adjuvants. Proc Natl Acad Sci U S A1995;92(5):1644-8.
[73] Sommer F, Wilken H, Faller G, Lohoff M. Systemic Th1immunization of mice againstHelicobacter pylori infection with CpG oligodeoxynucleotides as adjuvants does notprotect from infection but enhances gastritis. Infect Immun2004;72(2):1029-35.
[74] Moschos SA, Bramwell VW, Somavarapu S, Alpar HO. Comparativeimmunomodulatory properties of a chitosan-MDP adjuvant combination followingintranasal or intramuscular immunisation. Vaccine2005;23(16):1923-30.
[75] Tada H, Aiba S, Shibata K, Ohteki T, Takada H. Synergistic effect of Nod1and Nod2agonists with toll-like receptor agonists on human dendritic cells to generateinterleukin-12and T helper type1cells. Infect Immun2005;73(12):7967-76.
[76] ten Brinke A, van Schijndel G, Visser R, de Gruijl TD, Zwaginga JJ, van Ham SM.Monophosphoryl lipid A plus IFNgamma maturation of dendritic cells inducesantigen-specific CD8+cytotoxic T cells with high cytolytic potential. Cancer ImmunolImmunother2010;59(8):1185-95.
[77] Raghavan S, Svennerholm AM, Holmgren J. Effects of oral vaccination andimmunomodulation by cholera toxin on experimental Helicobacter pylori infection,reinfection, and gastritis. Infect Immun2002;70(8):4621-7.
[78] Weltzin R, Kleanthous H, Guirakhoo F, Monath TP, Lee CK. Novel intranasalimmunization techniques for antibody induction and protection of mice against gastricHelicobacter felis infection. Vaccine1997;15(4):370-6.
[79] Lee CK, Weltzin R, Thomas WD, Jr., Kleanthous H, Ermak TH, Soman G, et al. Oralimmunization with recombinant Helicobacter pylori urease induces secretory IgAantibodies and protects mice from challenge with Helicobacter felis. J Infect Dis1995;172(1):161-72.
[80] Nystrom J, Raghavan S, Svennerholm AM. Mucosal immune responses are related toreduction of bacterial colonization in the stomach after therapeutic Helicobacter pyloriimmunization in mice. Microbes Infect2006;8(2):442-9.
[81] Ikewaki J, Nishizono A, Goto T, Fujioka T, Mifune K. Therapeutic oral vaccinationinduces mucosal immune response sufficient to eliminate long-term Helicobacterpylori infection. Microbiol Immunol2000;44(1):29-39.
[82] Taylor JM, Ziman ME, Canfield DR, Vajdy M, Solnick JV. Effects of a Th1-versus aTh2-biased immune response in protection against Helicobacter pylori challenge inmice. Microb Pathog2008;44(1):20-7.
[83] Shi Y, Liu XF, Zhuang Y, Zhang JY, Liu T, Yin Z, et al. Helicobacter pylori-inducedTh17responses modulate Th1cell responses, benefit bacterial growth, and contributeto pathology in mice. J Immunol2010;184(9):5121-9.
[84] DeLyria ES, Redline RW, Blanchard TG. Vaccination of mice against H pylori inducesa strong Th-17response and immunity that is neutrophil dependent. Gastroenterology2009;136(1):247-56.
[85] Chen RT, Glasser JW, Rhodes PH, Davis RL, Barlow WE, Thompson RS, et al.Vaccine Safety Datalink project: a new tool for improving vaccine safety monitoring inthe United States. The Vaccine Safety Datalink Team. Pediatrics1997;99(6):765-73.
[86] Varricchio F, Iskander J, Destefano F, Ball R, Pless R, Braun MM, et al. Understandingvaccine safety information from the Vaccine Adverse Event Reporting System. PediatrInfect Dis J2004;23(4):287-94.
[87] Williams SE, Klein NP, Halsey N, Dekker CL, Baxter RP, Marchant CD, et al.Overview of the Clinical Consult Case Review of adverse events followingimmunization: Clinical Immunization Safety Assessment (CISA) network2004-2009.Vaccine2011;29(40):6920-7.
[88] Verdier F. Non-clinical vaccine safety assessment. Toxicology2002;174(1):37-43.
[89] Weibel RE, Benor DE. Chronic arthropathy and musculoskeletal symptoms associatedwith rubella vaccines. A review of124claims submitted to the National Vaccine InjuryCompensation Program. Arthritis Rheum1996;39(9):1529-34.
[90] Fritsche PJ, Helbling A, Ballmer-Weber BK. Vaccine hypersensitivity--update andoverview. Swiss Med Wkly2010;140(17-18):238-46.
[91] Zhang J, Delzell E, Xie F, Baddley JW, Spettell C, McMahan RM, et al. The use, safety,and effectiveness of herpes zoster vaccination in individuals with inflammatory andautoimmune diseases: a longitudinal observational study. Arthritis Res Ther2011;13(5):R174.
[92] Zhang J. T cell vaccination as an immunotherapy for autoimmune diseases. Cell MolImmunol2004;1(5):321-7.
[93] Chao C, Jacobsen SJ. Evaluation of autoimmune safety signal in observational vaccinesafety studies. Hum Vaccin Immunother2012;8(9):1302-4.
[94] Koenig HC, Sutherland A, Izurieta HS, McGonagle D. Application of theimmunological disease continuum to study autoimmune and other inflammatory eventsafter vaccination. Vaccine2011;29(5):913-9.
[95] Mohammed AR, Bramwell VW, Kirby DJ, McNeil SE, Perrie Y. Increased potential ofa cationic liposome-based delivery system: enhancing stability and sustainedimmunological activity in pre-clinical development. Eur J Pharm Biopharm2010;76(3):404-12.
[96] Thimmulappa RK, Scollick C, Traore K, Yates M, Trush MA, Liby KT, et al.Nrf2-dependent protection from LPS induced inflammatory response and mortality byCDDO-Imidazolide. Biochem Biophys Res Commun2006;351(4):883-9.
[97] Pilling AM, Harman RM, Jones SA, McCormack NA, Lavender D, Haworth R. Theassessment of local tolerance, acute toxicity, and DNA biodistribution followingparticle-mediated delivery of a DNA vaccine to minipigs. Toxicol Pathol2002;30(3):298-305.
[98] Oh H, Joung J, Kim BG, Nam KT, Hong SH, Song HC, et al. Improved protocols forhistamine sensitization testing of acellular pertussis vaccines. Vaccine2012;30(50):7246-52.
[99] Bhogal N. Immunotoxicity and immunogenicity of biopharmaceuticals: designconcepts and safety assessment. Curr Drug Saf2010;5(4):293-307.
[100] Putman E, van der Laan JW, van Loveren H. Assessing immunotoxicity: guidelines.Fundam Clin Pharmacol2003;17(5):615-26.
[101] Ikarashi Y, Ohno K, Momma J, Tsuchiya T, Nakamura A. Assessment of contactsensitivity of four thiourea rubber accelerators: comparison of two mouse lymph nodeassays with the guinea pig maximization test. Food Chem Toxicol1994;32(11):1067-72.
[102] Peng YY, Glattauer V, Ramshaw JA, Werkmeister JA. Evaluation of theimmunogenicity and cell compatibility of avian collagen for biomedical applications. JBiomed Mater Res A2010;93(4):1235-44.
[1] Ernst WA, Kim HJ, Tumpey TM, Jansen AD, Tai W, Cramer DV, et al. Protectionagainst H1, H5, H6and H9influenza A infection with liposomal matrix2epitopevaccines. Vaccine2006;24(24):5158-68.
[2] Wang F, Feng X, Zheng Q, Hou H, Cao R, Zhou B, et al. Multiple linear epitopes(B-cell, CTL and Th) of JEV expressed in recombinant MVA as multiple epitopevaccine induces a protective immune response. Virol J2012;9:204.
[3] Craiu A, Gaczynska M, Akopian T, Gramm CF, Fenteany G, Goldberg AL, et al.Lactacystin and clasto-lactacystin beta-lactone modify multiple proteasomebeta-subunits and inhibit intracellular protein degradation and major histocompatibilitycomplex class I antigen presentation. J Biol Chem1997;272(20):13437-45.
[4] Cunningham BC, Wells JA. High-resolution epitope mapping of hGH-receptorinteractions by alanine-scanning mutagenesis. Science1989;244(4908):1081-5.
[5] Schofield DJ, Pope AR, Clementel V, Buckell J, Chapple S, Clarke KF, et al.Application of phage display to high throughput antibody generation andcharacterization. Genome Biol2007;8(11):R254.
[6] Meister GE, Roberts CG, Berzofsky JA, De Groot AS. Two novel T cell epitopeprediction algorithms based on MHC-binding motifs; comparison of predicted andpublished epitopes from Mycobacterium tuberculosis and HIV protein sequences.Vaccine1995;13(6):581-91.
[7] Zhao Y, Pinilla C, Valmori D, Martin R, Simon R. Application of support vectormachines for T-cell epitopes prediction. Bioinformatics2003;19(15):1978-84.
[8] Guan P, Doytchinova IA, Zygouri C, Flower DR. MHCPred: A server for quantitativeprediction of peptide-MHC binding. Nucleic Acids Res2003;31(13):3621-4.
[9] Yu K, Petrovsky N, Schonbach C, Koh JY, Brusic V. Methods for prediction of peptidebinding to MHC molecules: a comparative study. Mol Med2002;8(3):137-48.
[10] Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sahin U, et al. Generation oftissue-specific and promiscuous HLA ligand databases using DNA microarrays andvirtual HLA class II matrices. Nat Biotechnol1999;17(6):555-61.
[11] Schafer JR, Jesdale BM, George JA, Kouttab NM, De Groot AS. Prediction ofwell-conserved HIV-1ligands using a matrix-based algorithm, EpiMatrix. Vaccine1998;16(19):1880-4.
[12] Raddrizzani L, Hammer J. Epitope scanning using virtual matrix-based algorithms.Brief Bioinform2000;1(2):179-89.
[13] Doytchinova IA, Flower DR. Towards the in silico identification of class II restrictedT-cell epitopes: a partial least squares iterative self-consistent algorithm for affinityprediction. Bioinformatics2003;19(17):2263-70.
[14] Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S. SYFPEITHI:database for MHC ligands and peptide motifs. Immunogenetics1999;50(3-4):213-9.
[15] Schuler MM, Nastke MD, Stevanovikc S. SYFPEITHI: database for searching andT-cell epitope prediction. Methods Mol Biol2007;409:75-93.
[16] Yang X, Yu X. An introduction to epitope prediction methods and software. Rev MedVirol2009;19(2):77-96.
[17] Iurescia S, Fioretti D, Fazio VM, Rinaldi M. Design and pre-clinical development ofepitope-based DNA vaccines against B-cell lymphoma. Curr Gene Ther2011;11(5):414-22.
[18] Rosa DS, Ribeiro SP, Cunha-Neto E. CD4+T cell epitope discovery and rationalvaccine design. Arch Immunol Ther Exp (Warsz)2010;58(2):121-30.
[19] Hayes AJ, Hughes CE, Caterson B. Antibodies and immunohistochemistry inextracellular matrix research. Methods2008;45(1):10-21.
[20] Honeyman MC, Brusic V, Stone NL, Harrison LC. Neural network-based prediction ofcandidate T-cell epitopes. Nat Biotechnol1998;16(10):966-9.
[21] De Groot AS, Bosma A, Chinai N, Frost J, Jesdale BM, Gonzalez MA, et al. Fromgenome to vaccine: in silico predictions, ex vivo verification. Vaccine2001;19(31):4385-95.
[22] Brusic V, Rudy G, Harrison LC. MHCPEP: a database of MHC-binding peptides.Nucleic Acids Res1994;22(17):3663-5.
[23] Nielsen M, Lund O. NN-align. An artificial neural network-based alignment algorithmfor MHC class II peptide binding prediction. BMC Bioinformatics2009;10:296.
[24] Lacerda M, Scheffler K, Seoighe C. Epitope discovery with phylogenetic hiddenMarkov models. Mol Biol Evol2010;27(5):1212-20.
[25] Bhasin M, Raghava GP. SVM based method for predicting HLA-DRB1*0401bindingpeptides in an antigen sequence. Bioinformatics2004;20(3):421-3.
[26] Tong JC, Tan TW, Ranganathan S. Modeling the structure of bound peptide ligands tomajor histocompatibility complex. Protein Sci2004;13(9):2523-32.
[27] Kurcinski M, Kolinski A. Steps towards flexible docking: modeling ofthree-dimensional structures of the nuclear receptors bound with peptide ligandsmimicking co-activators' sequences. J Steroid Biochem Mol Biol2007;103(3-5):357-60.
[28] Altuvia Y, Schueler O, Margalit H. Ranking potential binding peptides to MHCmolecules by a computational threading approach. J Mol Biol1995;249(2):244-50.
[29] Schueler-Furman O, Altuvia Y, Sette A, Margalit H. Structure-based prediction ofbinding peptides to MHC class I molecules: application to a broad range of MHCalleles. Protein Sci2000;9(9):1838-46.
[30] Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, et al. Limitations ofAb initio predictions of peptide binding to MHC class II molecules. PLoS One2010;5(2):e9272.
[31] Flower DR, Phadwal K, Macdonald IK, Coveney PV, Davies MN, Wan S. T-cellepitope prediction and immune complex simulation using molecular dynamics: state ofthe art and persisting challenges. Immunome Res2010;6Suppl2:S4.
[32] Nakamura Y, Tai S, Oshita C, Iizuka A, Ashizawa T, Saito S, et al. Analysis ofHLA-A24-restricted peptides of carcinoembryonic antigen using a novelstructure-based peptide-HLA docking algorithm. Cancer Sci2011;102(4):690-6.
[33] Rognan D, Scapozza L, Folkers G, Daser A. Molecular dynamics simulation ofMHC-peptide complexes as a tool for predicting potential T cell epitopes. Biochemistry1994;33(38):11476-85.
[34] Kim Y, Sette A, Peters B. Applications for T-cell epitope queries and tools in theImmune Epitope Database and Analysis Resource. J Immunol Methods2011;374(1-2):62-9.
[35] Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, et al. Immuneepitope database analysis resource. Nucleic Acids Res2012;40(Web Serverissue):W525-30.
[2] Peek RM, Jr., Crabtree JE. Helicobacter infection and gastric neoplasia. J Pathol2006;208(2):233-48.
[3] Chiba N, Rao BV, Rademaker JW, Hunt RH. Meta-analysis of the efficacy of antibiotictherapy in eradicating Helicobacter pylori. Am J Gastroenterol1992;87(12):1716-27.
[4] Graham DY, Fischbach L. Helicobacter pylori treatment in the era of increasingantibiotic resistance. Gut2010;59(8):1143-53.
[5] Hojsak I, Kos T, Dumancic J, Misak Z, Jadresin O, Jaklin Kekez A, et al. Antibioticresistance of Helicobacter pylori in pediatric patients--10years' experience. Eur JPediatr2012;171(9):1325-30.
[6] Lionetti E, Indrio F, Pavone L, Borrelli G, Cavallo L, Francavilla R. Role of probioticsin pediatric patients with Helicobacter pylori infection: a comprehensive review of theliterature. Helicobacter2010;15(2):79-87.
[7] Franceschi F, Cazzato A, Nista EC, Scarpellini E, Roccarina D, Gigante G, et al. Roleof probiotics in patients with Helicobacter pylori infection. Helicobacter2007;12Suppl2:59-63.
[8] Rupnow MF, Chang AH, Shachter RD, Owens DK, Parsonnet J. Cost-effectiveness ofa potential prophylactic Helicobacter pylori vaccine in the United States. J Infect Dis2009;200(8):1311-7.
[9] Czinn SJ, Blanchard T. Vaccinating against Helicobacter pylori infection. Nat RevGastroenterol Hepatol2011;8(3):133-40.
[10] Del Giudice G, Malfertheiner P, Rappuoli R. Development of vaccines againstHelicobacter pylori. Expert Rev Vaccines2009;8(8):1037-49.
[11] Liu KY, Shi Y, Luo P, Yu S, Chen L, Zhao Z, et al. Therapeutic efficacy of oralimmunization with attenuated Salmonella typhimurium expressing Helicobacter pyloriCagA, VacA and UreB fusion proteins in mice model. Vaccine2011;29(38):6679-85.
[12] DiPetrillo MD, Tibbetts T, Kleanthous H, Killeen KP, Hohmann EL. Safety andimmunogenicity of phoP/phoQ-deleted Salmonella typhi expressing Helicobacterpylori urease in adult volunteers. Vaccine1999;18(5-6):449-59.
[13] Metzger WG, Mansouri E, Kronawitter M, Diescher S, Soerensen M, Hurwitz R, et al.Impact of vector-priming on the immunogenicity of a live recombinant Salmonellaenterica serovar typhi Ty21a vaccine expressing urease A and B from Helicobacterpylori in human volunteers. Vaccine2004;22(17-18):2273-7.
[14] Marchetti M, Rossi M, Giannelli V, Giuliani MM, Pizza M, Censini S, et al. Protectionagainst Helicobacter pylori infection in mice by intragastric vaccination with H. pyloriantigens is achieved using a non-toxic mutant of E. coli heat-labile enterotoxin (LT) asadjuvant. Vaccine1998;16(1):33-7.
[15] Smythies LE, Novak MJ, Waites KB, Lindsey JR, Morrow CD, Smith PD. Poliovirusreplicons encoding the B subunit of Helicobacter pylori urease protect mice against H.pylori infection. Vaccine2005;23(7):901-9.
[16] Corthesy B, Boris S, Isler P, Grangette C, Mercenier A. Oral immunization of micewith lactic acid bacteria producing Helicobacter pylori urease B subunit partiallyprotects against challenge with Helicobacter felis. J Infect Dis2005;192(8):1441-9.
[17] Wu C, Shi Y, Guo H, Zou WY, Guo G, Xie QH, et al. Protection against Helicobacterpylori infection in mongolian gerbil by intragastric or intramuscular administration ofH. pylori multicomponent vaccine. Helicobacter2008;13(3):191-9.
[18] Zhang L, Yang Y, Yang X, Zhao J, Yang J, Liu F, et al. T cell epitope-basedpeptide-DNA dual vaccine induces protective immunity against Schistosomajaponicum infection in C57BL/6J mice. Microbes Infect2008;10(3):251-9.
[19] Sette A, Fikes J. Epitope-based vaccines: an update on epitope identification, vaccinedesign and delivery. Curr Opin Immunol2003;15(4):461-70.
[20] Goldstein G, Chicca JJ,2nd. A universal anti-HIV-1Tat epitope vaccine that is fullysynthetic and self-adjuvanting. Vaccine2010;28(4):1008-14.
[21] Ahlers JD, Belyakov IM. Lessons learned from natural infection: focusing on thedesign of protective T cell vaccines for HIV/AIDS. Trends Immunol2010;31(3):120-30.
[22] Ingram RJ, Metan G, Maillere B, Doganay M, Ozkul Y, Kim LU, et al. Naturalexposure to cutaneous anthrax gives long-lasting T cell immunity encompassinginfection-specific epitopes. J Immunol2010;184(7):3814-21.
[23] Jin X, Newman MJ, De-Rosa S, Cooper C, Thomas E, Keefer M, et al. A novel HIV Thelper epitope-based vaccine elicits cytokine-secreting HIV-specific CD4+T cells in aPhase I clinical trial in HIV-uninfected adults. Vaccine2009;27(50):7080-6.
[24] Paul S, Planque S, Nishiyama Y, Escobar M, Hanson C. Back to the future: covalentepitope-based HIV vaccine development. Expert Rev Vaccines2010;9(9):1027-43.
[25] Gupta SK, Smita S, Sarangi AN, Srivastava M, Akhoon BA, Rahman Q. In silicoCD4+T-cell epitope prediction and HLA distribution analysis for the potential proteinsof Neisseria meningitidis Serogroup B--a clue for vaccine development. Vaccine2010;28(43):7092-7.
[26] McNamara LA, He Y, Yang Z. Using epitope predictions to evaluate efficacy andpopulation coverage of the Mtb72f vaccine for tuberculosis. BMC Immunol2010;11:18.
[27] Zhou WY, Shi Y, Wu C, Zhang WJ, Mao XH, Guo G, et al. Therapeutic efficacy of amulti-epitope vaccine against Helicobacter pylori infection in BALB/c mice model.Vaccine2009;27(36):5013-9.
[28][28] Moss SF, Moise L, Lee DS, Kim W, Zhang S, Lee J, et al. HelicoVax:epitope-based therapeutic Helicobacter pylori vaccination in a mouse model. Vaccine2011;29(11):2085-91.
[29] Flach CF, Svensson N, Blomquist M, Ekman A, Raghavan S, Holmgren J. A truncatedform of HpaA is a promising antigen for use in a vaccine against Helicobacter pylori.Vaccine2011;29(6):1235-41.
[30] Sutton P, Doidge C, Pinczower G, Wilson J, Harbour S, Swierczak A, et al.Effectiveness of vaccination with recombinant HpaA from Helicobacter pylori isinfluenced by host genetic background. FEMS Immunol Med Microbiol2007;50(2):213-9.
[31] Zhang H, Liu M, Li Y, Zhao Y, He H, Yang G, et al. Oral immunogenicity andprotective efficacy in mice of a carrot-derived vaccine candidate expressing UreBsubunit against Helicobacter pylori. Protein Expr Purif2010;69(2):127-31.
[32] Lee MH, Roussel Y, Wilks M, Tabaqchali S. Expression of Helicobacter pylori ureasesubunit B gene in Lactococcus lactis MG1363and its use as a vaccine delivery systemagainst H. pylori infection in mice. Vaccine2001;19(28-29):3927-35.
[33] Rossi G, Ruggiero P, Peppoloni S, Pancotto L, Fortuna D, Lauretti L, et al. Therapeuticvaccination against Helicobacter pylori in the beagle dog experimental model: safety,immunogenicity, and efficacy. Infect Immun2004;72(6):3252-9.
[34] Sayi A, Kohler E, Hitzler I, Arnold I, Schwendener R, Rehrauer H, et al. The CD4+Tcell-mediated IFN-gamma response to Helicobacter infection is essential for clearanceand determines gastric cancer risk. J Immunol2009;182(11):7085-101.
[35] Ermak TH, Giannasca PJ, Nichols R, Myers GA, Nedrud J, Weltzin R, et al.Immunization of mice with urease vaccine affords protection against Helicobacterpylori infection in the absence of antibodies and is mediated by MHC class II-restrictedresponses. J Exp Med1998;188(12):2277-88.
[36] Allison CC, Ferrero RL. Role of virulence factors and host cell signaling in therecognition of Helicobacter pylori and the generation of immune responses. FutureMicrobiol2010;5(8):1233-55.
[37] Prinz C, Hafsi N, Voland P. Helicobacter pylori virulence factors and the host immuneresponse: implications for therapeutic vaccination. Trends Microbiol2003;11(3):134-8.
[38] Kim Y, Sette A, Peters B. Applications for T-cell epitope queries and tools in theImmune Epitope Database and Analysis Resource. J Immunol Methods2011;374(1-2):62-9.
[39] Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, et al. Immuneepitope database analysis resource. Nucleic Acids Res2012;40(Web Serverissue):W525-30.
[40] Iankov ID, Haralambieva IH, Galanis E. Immunogenicity of attenuated measles virusengineered to express Helicobacter pylori neutrophil-activating protein. Vaccine2011;29(8):1710-20.
[41] Craiu A, Gaczynska M, Akopian T, Gramm CF, Fenteany G, Goldberg AL, et al.Lactacystin and clasto-lactacystin beta-lactone modify multiple proteasomebeta-subunits and inhibit intracellular protein degradation and major histocompatibilitycomplex class I antigen presentation. J Biol Chem1997;272(20):13437-45.
[42] Cunningham BC, Wells JA. High-resolution epitope mapping of hGH-receptorinteractions by alanine-scanning mutagenesis. Science1989;244(4908):1081-5.
[43] Schofield DJ, Pope AR, Clementel V, Buckell J, Chapple S, Clarke KF, et al.Application of phage display to high throughput antibody generation andcharacterization. Genome Biol2007;8(11):R254.
[44] Fridman A, Finnefrock AC, Peruzzi D, Pak I, La Monica N, Bagchi A, et al. Anefficient T-cell epitope discovery strategy using in silico prediction and the iTopiaassay platform. Oncoimmunology2012;1(8):1258-70.
[45] Bernardeau K, Kerzhero J, Fortun A, Moreau-Aubry A, Favry E, Echasserieau K, et al.A simple competitive assay to determine peptide affinity for HLA class II molecules: auseful tool for epitope prediction. J Immunol Methods2011;371(1-2):97-105.
[46] Sabarth N, Hurwitz R, Meyer TF, Bumann D. Multiparameter selection of Helicobacterpylori antigens identifies two novel antigens with high protective efficacy. InfectImmun2002;70(11):6499-503.
[47] Charoentong P, Angelova M, Efremova M, Gallasch R, Hackl H, Galon J, et al.Bioinformatics for cancer immunology and immunotherapy. Cancer ImmunolImmunother2012;61(11):1885-903.
[48] Batori V, Friis EP, Nielsen H, Roggen EL. An in silico method using an epitope motifdatabase for predicting the location of antigenic determinants on proteins in a structuralcontext. J Mol Recognit2006;19(1):21-9.
[49] Bhasin M, Raghava GP. Prediction of CTL epitopes using QM, SVM and ANNtechniques. Vaccine2004;22(23-24):3195-204.
[50] Vider-Shalit T, Louzoun Y. MHC-I prediction using a combination of T cell epitopesand MHC-I binding peptides. J Immunol Methods2011;374(1-2):43-6.
[51] Ravindra R, Zhao S, Gies H, Winter R. Protein encapsulation in mesoporous silicate:the effects of confinement on protein stability, hydration, and volumetric properties. JAm Chem Soc2004;126(39):12224-5.
[52] Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalablemolecular dynamics with NAMD. J Comput Chem2005;26(16):1781-802.
[53] Wang Y, Harrison CB, Schulten K, McCammon JA. Implementation of AcceleratedMolecular Dynamics in NAMD. Comput Sci Discov2011;4(1).
[54] Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph1996;14(1):33-8,27-8.
[55] Zhuang Z, Peng Q, Li Y. Controlled synthesis of semiconductor nanostructures in theliquid phase. Chem Soc Rev2011;40(11):5492-513.
[56] Friligou I, Papadimitriou E, Gatos D, Matsoukas J, Tselios T. Microwave-assistedsolid-phase peptide synthesis of the60-110domain of human pleiotrophin on2-chlorotrityl resin. Amino Acids2011;40(5):1431-40.
[57] Pattabiraman VR, Ogunkoya AO, Bode JW. Chemical Protein Synthesis byChemoselective alpha-Ketoacid-Hydroxylamine (KAHA) Ligations with5-Oxaproline.Angew Chem Int Ed Engl2012.
[58] Hunt I. From gene to protein: a review of new and enabling technologies formulti-parallel protein expression. Protein Expr Purif2005;40(1):1-22.
[59] Li J, Menzel C, Meier D, Zhang C, Dubel S, Jostock T. A comparative study ofdifferent vector designs for the mammalian expression of recombinant IgG antibodies.J Immunol Methods2007;318(1-2):113-24.
[60] Sorensen HP, Mortensen KK. Advanced genetic strategies for recombinant proteinexpression in Escherichia coli. J Biotechnol2005;115(2):113-28.
[61] Ventura S, Villaverde A. Protein quality in bacterial inclusion bodies. TrendsBiotechnol2006;24(4):179-85.
[62][62] Weiner AJ, Geysen HM, Christopherson C, Hall JE, Mason TJ, Saracco G, et al.Evidence for immune selection of hepatitis C virus (HCV) putative envelopeglycoprotein variants: potential role in chronic HCV infections. Proc Natl Acad Sci US A1992;89(8):3468-72.
[63] Calvo-Calle JM, Oliveira GA, Watta CO, Soverow J, Parra-Lopez C, Nardin EH. Alinear peptide containing minimal T-and B-cell epitopes of Plasmodium falciparumcircumsporozoite protein elicits protection against transgenic sporozoite challenge.Infect Immun2006;74(12):6929-39.
[64] Singh SM, Panda AK. Solubilization and refolding of bacterial inclusion body proteins.J Biosci Bioeng2005;99(4):303-10.
[65] Lilie H, Schwarz E, Rudolph R. Advances in refolding of proteins produced in E. coli.Curr Opin Biotechnol1998;9(5):497-501.
[66] Tsumoto K, Ejima D, Kumagai I, Arakawa T. Practical considerations in refoldingproteins from inclusion bodies. Protein Expr Purif2003;28(1):1-8.
[67] Kramberger P, Peterka M, Boben J, Ravnikar M, Strancar A. Short monolithiccolumns--a breakthrough in purification and fast quantification of tomato mosaic virus.J Chromatogr A2007;1144(1):143-9.
[68] Lehmberg E, Traina JA, Chakel JA, Chang RJ, Parkman M, McCaman MT, et al.Reversed-phase high-performance liquid chromatographic assay for the adenovirustype5proteome. J Chromatogr B Biomed Sci Appl1999;732(2):411-23.
[69] Eisenberg JC, Czinn SJ, Garhart CA, Redline RW, Bartholomae WC, Gottwein JM, etal. Protective efficacy of anti-Helicobacter pylori immunity following systemicimmunization of neonatal mice. Infect Immun2003;71(4):1820-7.
[70] Gottwein JM, Blanchard TG, Targoni OS, Eisenberg JC, Zagorski BM, Redline RW, etal. Protective anti-Helicobacter immunity is induced with aluminum hydroxide orcomplete Freund's adjuvant by systemic immunization. J Infect Dis2001;184(3):308-14.
[71] Guy B, Hessler C, Fourage S, Haensler J, Vialon-Lafay E, Rokbi B, et al. Systemicimmunization with urease protects mice against Helicobacter pylori infection. Vaccine1998;16(8):850-6.
[72] Douce G, Turcotte C, Cropley I, Roberts M, Pizza M, Domenghini M, et al. Mutants ofEscherichia coli heat-labile toxin lacking ADP-ribosyltransferase activity act asnontoxic, mucosal adjuvants. Proc Natl Acad Sci U S A1995;92(5):1644-8.
[73] Sommer F, Wilken H, Faller G, Lohoff M. Systemic Th1immunization of mice againstHelicobacter pylori infection with CpG oligodeoxynucleotides as adjuvants does notprotect from infection but enhances gastritis. Infect Immun2004;72(2):1029-35.
[74] Moschos SA, Bramwell VW, Somavarapu S, Alpar HO. Comparativeimmunomodulatory properties of a chitosan-MDP adjuvant combination followingintranasal or intramuscular immunisation. Vaccine2005;23(16):1923-30.
[75] Tada H, Aiba S, Shibata K, Ohteki T, Takada H. Synergistic effect of Nod1and Nod2agonists with toll-like receptor agonists on human dendritic cells to generateinterleukin-12and T helper type1cells. Infect Immun2005;73(12):7967-76.
[76] ten Brinke A, van Schijndel G, Visser R, de Gruijl TD, Zwaginga JJ, van Ham SM.Monophosphoryl lipid A plus IFNgamma maturation of dendritic cells inducesantigen-specific CD8+cytotoxic T cells with high cytolytic potential. Cancer ImmunolImmunother2010;59(8):1185-95.
[77] Raghavan S, Svennerholm AM, Holmgren J. Effects of oral vaccination andimmunomodulation by cholera toxin on experimental Helicobacter pylori infection,reinfection, and gastritis. Infect Immun2002;70(8):4621-7.
[78] Weltzin R, Kleanthous H, Guirakhoo F, Monath TP, Lee CK. Novel intranasalimmunization techniques for antibody induction and protection of mice against gastricHelicobacter felis infection. Vaccine1997;15(4):370-6.
[79] Lee CK, Weltzin R, Thomas WD, Jr., Kleanthous H, Ermak TH, Soman G, et al. Oralimmunization with recombinant Helicobacter pylori urease induces secretory IgAantibodies and protects mice from challenge with Helicobacter felis. J Infect Dis1995;172(1):161-72.
[80] Nystrom J, Raghavan S, Svennerholm AM. Mucosal immune responses are related toreduction of bacterial colonization in the stomach after therapeutic Helicobacter pyloriimmunization in mice. Microbes Infect2006;8(2):442-9.
[81] Ikewaki J, Nishizono A, Goto T, Fujioka T, Mifune K. Therapeutic oral vaccinationinduces mucosal immune response sufficient to eliminate long-term Helicobacterpylori infection. Microbiol Immunol2000;44(1):29-39.
[82] Taylor JM, Ziman ME, Canfield DR, Vajdy M, Solnick JV. Effects of a Th1-versus aTh2-biased immune response in protection against Helicobacter pylori challenge inmice. Microb Pathog2008;44(1):20-7.
[83] Shi Y, Liu XF, Zhuang Y, Zhang JY, Liu T, Yin Z, et al. Helicobacter pylori-inducedTh17responses modulate Th1cell responses, benefit bacterial growth, and contributeto pathology in mice. J Immunol2010;184(9):5121-9.
[84] DeLyria ES, Redline RW, Blanchard TG. Vaccination of mice against H pylori inducesa strong Th-17response and immunity that is neutrophil dependent. Gastroenterology2009;136(1):247-56.
[85] Chen RT, Glasser JW, Rhodes PH, Davis RL, Barlow WE, Thompson RS, et al.Vaccine Safety Datalink project: a new tool for improving vaccine safety monitoring inthe United States. The Vaccine Safety Datalink Team. Pediatrics1997;99(6):765-73.
[86] Varricchio F, Iskander J, Destefano F, Ball R, Pless R, Braun MM, et al. Understandingvaccine safety information from the Vaccine Adverse Event Reporting System. PediatrInfect Dis J2004;23(4):287-94.
[87] Williams SE, Klein NP, Halsey N, Dekker CL, Baxter RP, Marchant CD, et al.Overview of the Clinical Consult Case Review of adverse events followingimmunization: Clinical Immunization Safety Assessment (CISA) network2004-2009.Vaccine2011;29(40):6920-7.
[88] Verdier F. Non-clinical vaccine safety assessment. Toxicology2002;174(1):37-43.
[89] Weibel RE, Benor DE. Chronic arthropathy and musculoskeletal symptoms associatedwith rubella vaccines. A review of124claims submitted to the National Vaccine InjuryCompensation Program. Arthritis Rheum1996;39(9):1529-34.
[90] Fritsche PJ, Helbling A, Ballmer-Weber BK. Vaccine hypersensitivity--update andoverview. Swiss Med Wkly2010;140(17-18):238-46.
[91] Zhang J, Delzell E, Xie F, Baddley JW, Spettell C, McMahan RM, et al. The use, safety,and effectiveness of herpes zoster vaccination in individuals with inflammatory andautoimmune diseases: a longitudinal observational study. Arthritis Res Ther2011;13(5):R174.
[92] Zhang J. T cell vaccination as an immunotherapy for autoimmune diseases. Cell MolImmunol2004;1(5):321-7.
[93] Chao C, Jacobsen SJ. Evaluation of autoimmune safety signal in observational vaccinesafety studies. Hum Vaccin Immunother2012;8(9):1302-4.
[94] Koenig HC, Sutherland A, Izurieta HS, McGonagle D. Application of theimmunological disease continuum to study autoimmune and other inflammatory eventsafter vaccination. Vaccine2011;29(5):913-9.
[95] Mohammed AR, Bramwell VW, Kirby DJ, McNeil SE, Perrie Y. Increased potential ofa cationic liposome-based delivery system: enhancing stability and sustainedimmunological activity in pre-clinical development. Eur J Pharm Biopharm2010;76(3):404-12.
[96] Thimmulappa RK, Scollick C, Traore K, Yates M, Trush MA, Liby KT, et al.Nrf2-dependent protection from LPS induced inflammatory response and mortality byCDDO-Imidazolide. Biochem Biophys Res Commun2006;351(4):883-9.
[97] Pilling AM, Harman RM, Jones SA, McCormack NA, Lavender D, Haworth R. Theassessment of local tolerance, acute toxicity, and DNA biodistribution followingparticle-mediated delivery of a DNA vaccine to minipigs. Toxicol Pathol2002;30(3):298-305.
[98] Oh H, Joung J, Kim BG, Nam KT, Hong SH, Song HC, et al. Improved protocols forhistamine sensitization testing of acellular pertussis vaccines. Vaccine2012;30(50):7246-52.
[99] Bhogal N. Immunotoxicity and immunogenicity of biopharmaceuticals: designconcepts and safety assessment. Curr Drug Saf2010;5(4):293-307.
[100] Putman E, van der Laan JW, van Loveren H. Assessing immunotoxicity: guidelines.Fundam Clin Pharmacol2003;17(5):615-26.
[101] Ikarashi Y, Ohno K, Momma J, Tsuchiya T, Nakamura A. Assessment of contactsensitivity of four thiourea rubber accelerators: comparison of two mouse lymph nodeassays with the guinea pig maximization test. Food Chem Toxicol1994;32(11):1067-72.
[102] Peng YY, Glattauer V, Ramshaw JA, Werkmeister JA. Evaluation of theimmunogenicity and cell compatibility of avian collagen for biomedical applications. JBiomed Mater Res A2010;93(4):1235-44.
[1] Ernst WA, Kim HJ, Tumpey TM, Jansen AD, Tai W, Cramer DV, et al. Protectionagainst H1, H5, H6and H9influenza A infection with liposomal matrix2epitopevaccines. Vaccine2006;24(24):5158-68.
[2] Wang F, Feng X, Zheng Q, Hou H, Cao R, Zhou B, et al. Multiple linear epitopes(B-cell, CTL and Th) of JEV expressed in recombinant MVA as multiple epitopevaccine induces a protective immune response. Virol J2012;9:204.
[3] Craiu A, Gaczynska M, Akopian T, Gramm CF, Fenteany G, Goldberg AL, et al.Lactacystin and clasto-lactacystin beta-lactone modify multiple proteasomebeta-subunits and inhibit intracellular protein degradation and major histocompatibilitycomplex class I antigen presentation. J Biol Chem1997;272(20):13437-45.
[4] Cunningham BC, Wells JA. High-resolution epitope mapping of hGH-receptorinteractions by alanine-scanning mutagenesis. Science1989;244(4908):1081-5.
[5] Schofield DJ, Pope AR, Clementel V, Buckell J, Chapple S, Clarke KF, et al.Application of phage display to high throughput antibody generation andcharacterization. Genome Biol2007;8(11):R254.
[6] Meister GE, Roberts CG, Berzofsky JA, De Groot AS. Two novel T cell epitopeprediction algorithms based on MHC-binding motifs; comparison of predicted andpublished epitopes from Mycobacterium tuberculosis and HIV protein sequences.Vaccine1995;13(6):581-91.
[7] Zhao Y, Pinilla C, Valmori D, Martin R, Simon R. Application of support vectormachines for T-cell epitopes prediction. Bioinformatics2003;19(15):1978-84.
[8] Guan P, Doytchinova IA, Zygouri C, Flower DR. MHCPred: A server for quantitativeprediction of peptide-MHC binding. Nucleic Acids Res2003;31(13):3621-4.
[9] Yu K, Petrovsky N, Schonbach C, Koh JY, Brusic V. Methods for prediction of peptidebinding to MHC molecules: a comparative study. Mol Med2002;8(3):137-48.
[10] Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sahin U, et al. Generation oftissue-specific and promiscuous HLA ligand databases using DNA microarrays andvirtual HLA class II matrices. Nat Biotechnol1999;17(6):555-61.
[11] Schafer JR, Jesdale BM, George JA, Kouttab NM, De Groot AS. Prediction ofwell-conserved HIV-1ligands using a matrix-based algorithm, EpiMatrix. Vaccine1998;16(19):1880-4.
[12] Raddrizzani L, Hammer J. Epitope scanning using virtual matrix-based algorithms.Brief Bioinform2000;1(2):179-89.
[13] Doytchinova IA, Flower DR. Towards the in silico identification of class II restrictedT-cell epitopes: a partial least squares iterative self-consistent algorithm for affinityprediction. Bioinformatics2003;19(17):2263-70.
[14] Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S. SYFPEITHI:database for MHC ligands and peptide motifs. Immunogenetics1999;50(3-4):213-9.
[15] Schuler MM, Nastke MD, Stevanovikc S. SYFPEITHI: database for searching andT-cell epitope prediction. Methods Mol Biol2007;409:75-93.
[16] Yang X, Yu X. An introduction to epitope prediction methods and software. Rev MedVirol2009;19(2):77-96.
[17] Iurescia S, Fioretti D, Fazio VM, Rinaldi M. Design and pre-clinical development ofepitope-based DNA vaccines against B-cell lymphoma. Curr Gene Ther2011;11(5):414-22.
[18] Rosa DS, Ribeiro SP, Cunha-Neto E. CD4+T cell epitope discovery and rationalvaccine design. Arch Immunol Ther Exp (Warsz)2010;58(2):121-30.
[19] Hayes AJ, Hughes CE, Caterson B. Antibodies and immunohistochemistry inextracellular matrix research. Methods2008;45(1):10-21.
[20] Honeyman MC, Brusic V, Stone NL, Harrison LC. Neural network-based prediction ofcandidate T-cell epitopes. Nat Biotechnol1998;16(10):966-9.
[21] De Groot AS, Bosma A, Chinai N, Frost J, Jesdale BM, Gonzalez MA, et al. Fromgenome to vaccine: in silico predictions, ex vivo verification. Vaccine2001;19(31):4385-95.
[22] Brusic V, Rudy G, Harrison LC. MHCPEP: a database of MHC-binding peptides.Nucleic Acids Res1994;22(17):3663-5.
[23] Nielsen M, Lund O. NN-align. An artificial neural network-based alignment algorithmfor MHC class II peptide binding prediction. BMC Bioinformatics2009;10:296.
[24] Lacerda M, Scheffler K, Seoighe C. Epitope discovery with phylogenetic hiddenMarkov models. Mol Biol Evol2010;27(5):1212-20.
[25] Bhasin M, Raghava GP. SVM based method for predicting HLA-DRB1*0401bindingpeptides in an antigen sequence. Bioinformatics2004;20(3):421-3.
[26] Tong JC, Tan TW, Ranganathan S. Modeling the structure of bound peptide ligands tomajor histocompatibility complex. Protein Sci2004;13(9):2523-32.
[27] Kurcinski M, Kolinski A. Steps towards flexible docking: modeling ofthree-dimensional structures of the nuclear receptors bound with peptide ligandsmimicking co-activators' sequences. J Steroid Biochem Mol Biol2007;103(3-5):357-60.
[28] Altuvia Y, Schueler O, Margalit H. Ranking potential binding peptides to MHCmolecules by a computational threading approach. J Mol Biol1995;249(2):244-50.
[29] Schueler-Furman O, Altuvia Y, Sette A, Margalit H. Structure-based prediction ofbinding peptides to MHC class I molecules: application to a broad range of MHCalleles. Protein Sci2000;9(9):1838-46.
[30] Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, et al. Limitations ofAb initio predictions of peptide binding to MHC class II molecules. PLoS One2010;5(2):e9272.
[31] Flower DR, Phadwal K, Macdonald IK, Coveney PV, Davies MN, Wan S. T-cellepitope prediction and immune complex simulation using molecular dynamics: state ofthe art and persisting challenges. Immunome Res2010;6Suppl2:S4.
[32] Nakamura Y, Tai S, Oshita C, Iizuka A, Ashizawa T, Saito S, et al. Analysis ofHLA-A24-restricted peptides of carcinoembryonic antigen using a novelstructure-based peptide-HLA docking algorithm. Cancer Sci2011;102(4):690-6.
[33] Rognan D, Scapozza L, Folkers G, Daser A. Molecular dynamics simulation ofMHC-peptide complexes as a tool for predicting potential T cell epitopes. Biochemistry1994;33(38):11476-85.
[34] Kim Y, Sette A, Peters B. Applications for T-cell epitope queries and tools in theImmune Epitope Database and Analysis Resource. J Immunol Methods2011;374(1-2):62-9.
[35] Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, et al. Immuneepitope database analysis resource. Nucleic Acids Res2012;40(Web Serverissue):W525-30.