iVAX: An integrated toolkit for the selection and optimization of antigens and the design of epitope-driven vaccines

References

• Jaiswal V, Chanumolu SK, Gupta A, Chauhan RS, Rout C. Jenner-predict server, prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. BMC Bioinformatics. 2013; 14,211; PMID,23815072; http,//dx.doi.org/10.1186/1471-2105-14-211
   PubMed Web of Science ®Google Scholar
• Doytchinova IA, Flower DR. VaxiJen, a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics. 2007; 8,4; PMID,17207271; http,//dx.doi.org/10.1186/1471-2105-8-4
   PubMed Web of Science ®Google Scholar
• Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B. The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 2015 Jan;43 (Database issue),D405-12; http,//dx.doi.org/10.1093/nar/gku938
   PubMed Web of Science ®Google Scholar
• A.S. De Groot, and W. Martin. From immunome to vaccine, epitope mapping and vaccine design tools. In, Novartis Foundation. Immunoinformatics, bioinformatic strategies for better understanding of immune function. Editors Petrovsky and Brusic. Novartis Found Symp 2003; 254; PMID,14712932
   PubMedGoogle Scholar
• Petrovsky N, Brusic V. Computational immunology, the coming of age. Immunol Cell Biol 2002; 80,248-54; PMID,12067412; http,//dx.doi.org/10.1046/j.1440-1711.2002.01093.x
   PubMed Web of Science ®Google Scholar
• Rappuoli R, and Covacci A. Reverse vaccinology and genomics. Science. 2003; 302,602; PMID,14576423; http,//dx.doi.org/10.1126/science.1092329
   PubMed Web of Science ®Google Scholar
• Pederson T. The immunome. Mol Immunol 1999; 36,1127-8; PMID,10698314; http,//dx.doi.org/10.1016/S0161-5890(99)00125-X
   PubMed Web of Science ®Google Scholar
• Doytchinova IA, Taylor P, Flower DR. Proteomics in vaccinology and immunobiology, an informatics perspective of the immunone. J Biomed Biotechnol 2003; 2003,267-90; PMID,14688414; http,//dx.doi.org/10.1155/S1110724303209232
   PubMedGoogle Scholar
• De Groot AS, McMurry J, Marcon L, Franco J, Rivera D, Kutzler M, Weiner D, Martin B. Developing an epitope-driven tuberculosis (TB) vaccine. Vaccine 2005; 23,2121-31; PMID,15755582; http,//dx.doi.org/10.1016/j.vaccine.2005.01.059
   PubMed Web of Science ®Google Scholar
• De Groot AS, Marcon L, Bishop EA, Rivera D, Kutzler M, Weiner DB, Martin W. HIV vaccine development by computer assisted design, the GAIA vaccine. Vaccine 2005; 23,2136-48; PMID,15755584; http,//dx.doi.org/10.1016/j.vaccine.2005.01.097
   PubMed Web of Science ®Google Scholar
• Otero M, Calarota SA, Dai A, De Groot AS, Boyer JD, Weiner DB. Efficacy of novel plasmid DNA encoding vaccinia antigens in improving current smallpox vaccination strategy. Vaccine 2006; 24,4461-70; PMID,16137803; http,//dx.doi.org/10.1016/j.vaccine.2005.08.010
   PubMed Web of Science ®Google Scholar
• De Groot AS, Ardito M, Moise L, Gustafson EA, Spero D, Tejada G, Martin W. Immunogenic consensus sequence T helper epitopes for pan-Burkholderia biodefense vaccine. Immunome Res 2011; 7,7
   PubMedGoogle Scholar
• Schanen BC, De Groot AS, Moise L, Ardito M, McClaine E, Martin W, Wittman V, Warren WL, Drake DR 3rd. Coupling sensitive in vitro and in silico techniques to assess cross-reactive CD4+ T cells against the swine-origin H1N1 influenza virus. Vaccine 2011; 29,3299-309; PMID,21349362; http,//dx.doi.org/10.1016/j.vaccine.2011.02.019
   PubMed Web of Science ®Google Scholar
• De Groot AS, Ardito M, McClaine E, Moise L, Martin WD. Immunoinformatic comparison of T-cell epitopes contained in novel swine-origin influenza A (H1N1) virus with epitopes in 2008–09 conventional influenza vaccine. Vaccine 2009; 27,5740-7; PMID,19660593; http,//dx.doi.org/10.1016/j.vaccine.2009.07.040
   PubMed Web of Science ®Google Scholar
• Levitz L, Koita OA, Sangare K, Ardito MT, Boyle CM, Rozehnal J, Tounkara K, Dao SM, Koné Y, Koty Z, et al. Conservation of HIV-1 T cell epitopes across time and clades, validation of HLA-A2 epitopes selected for the GAIA HIV vaccine. Vaccine. 2012; 30,7547-60; PMID,23102976; http,//dx.doi.org/10.1016/j.vaccine.2012.10.042
   PubMed Web of Science ®Google Scholar
• De Groot AS, Levitz L, Ardito MT, Skowron G, Mayer KH, Buus S, Boyle CM, Martin WD. Further progress on defining highly conserved immunogenic epitopes for a global HIV vaccine, HLA-A3-restricted GAIA vaccine epitopes. Hum Vaccin Immunother 2012; 8,987-1000; PMID,22777092
   PubMed Web of Science ®Google Scholar
• Alexander J, Bilsel P, del Guercio MF, Marinkovic-Petrovic A, Southwood S, Stewart S, Ishioka G, Kotturi MF, Botten J, Sidney J, et al. Identification of broad binding class I HLA supertype epitopes to provide universal coverage of influenza A virus. Hum Immunol 2010; 71,468-74; PMID,20156506
   PubMed Web of Science ®Google Scholar
• Zhang GL, Riemer AB, Keskin DB, Chitkushev L, Reinherz EL, Brusic V. HPVdb, a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology. Database (Oxford) 2014; 2014, bau031; PMID,24705205
   PubMedGoogle Scholar
• Rajapaksha H, Petrovsky N. In Silico structural homology modelling and docking for assessment of pandemic potential of a novel H7N9 influenza virus and its ability to be neutralized by existing anti-hemagglutinin antibodies. PLoS One 2014; 9,e102618; PMID,25047593
   PubMedGoogle Scholar
• Molero-Abraham M, Lafuente EM, Flower DR, Reche PA. Selection of conserved epitopes from hepatitis C virus for pan-populational stimulation of T-cell responses. Clin Dev Immunol 2013; 2013,601943; PMID,24348677
   PubMed Web of Science ®Google Scholar
• Xiang Z, He Y. Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinformatics 2013; 14 Suppl 4,S2s
   Web of Science ®Google Scholar
• Moise L, Buller RM, Schriewer J, Lee J, Frey SE, Weiner DB, Martin W, De Groot AS. VennVax, a DNA-prime, peptide-boost multi-T-cell epitope poxvirus vaccine, induces protective immunity against vaccinia infection by T cell response alone. Vaccine 2011; 29,501-11; PMID,21055490
   PubMed Web of Science ®Google Scholar
• Moss SF, Moise L, Lee DS, Kim W, Zhang S, Lee J, Rogers AB, Martin W, De Groot AS. HelicoVax, epitope-based therapeutic H. pylori vaccination in a mouse model of gastric cancer. Vaccine 2011 ;29,2085-91; PMID,21236233
   PubMed Web of Science ®Google Scholar
• Moise L, Gutierrez AH, Bailey-Kellogg C, Terry F, Leng Q, Abdel Hady KM, VerBerkmoes NC, Sztein MB, Losikoff PT, Martin WD, et al. The two-faced T cell epitope, examining the host-microbe interface with JanusMatrix. Hum Vaccin Immunother 2013; 9,1577-86; PMID,23584251
   PubMed Web of Science ®Google Scholar
• Losikoff PT, Mishra S, Terry F, Gutierrez A, Ardito MT, Fast L, Nevola M, Martin WD, Bailey-Kellogg C, De Groot AS, Gregory SH. HCV Epitope, homologous to multiple human protein sequences, induces a regulatory T cell response in infected patients. J Hepatol. 2015; 62(1),48-55; PMID,25157982
   PubMed Web of Science ®Google Scholar
• Elfaki ME, Khalil EA, Degroot AS, Musa AM, Gutierrez A, Younis BM, Salih KA, El-Hassan AM. Immunogenicity and immune modulatory effects of in silico predicted L. donovani candidate peptide vaccines. Hum Vaccin Immunother 2012; 8,1769-74; PMID,22922767
   PubMed Web of Science ®Google Scholar
• Poland GA. Vaccines against Lyme disease, what happened and what lessons can we learn? Clin Infect Dis 2011; 52,s253-8; PMID,21217172
   PubMed Web of Science ®Google Scholar
• He Y, Racz R, Sayers S, Lin Y, Todd T, Hur J, Li X, Patel M, Zhao B, Chung M, et al. Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Res 2014; 42(Database issue),D1124-32; PMID,24259431
   PubMedGoogle Scholar
• Liu R, Desrosiers J, Martin BA, Moise L, De Groot AS. Immunogenicity assessment of in silico-selected T cell epitopes for a Burkholderia biodefense vaccine. American Society for Microbiology (ASM) Biodefense and Emerging Diseases. J Immunol 2013; 190 (Meeting Abstract Supplement) 54.10
   Google Scholar
• Zhang S, Desrosiers J, Aponte-Pieras JR, DaSilva K, Fast LD, Terry F, Martin WD, De Groot AS, Moise L, Moss SF. Human immune responses to H. pylori HLA class II epitopes identified by immunoinformatic methods. PLoS One 2014; 9,e94974; PMID,24740005
   PubMed Web of Science ®Google Scholar
• Mishra S, Losikoff PT, Self AA, Terry F, Ardito MT, Tassone R, Martin WD, De Groot AS, Gregory SH. Peptide-pulsed dendritic cells induce the hepatitis C viral epitope-specific responses of naïve human T cells. Vaccine 2014; 32,3285-92; PMID,24721533; http,//dx.doi.org/10.1016/j.vaccine.2014.03.083
   PubMed Web of Science ®Google Scholar
• Abdel-Hady KM, Gutierrez AH, Terry F, Desrosiers J, De Groot AS, Azzazy HM. Identification and retrospective validation of T-cell epitopes in the hepatitis C virus genotype 4 proteome, An accelerated approach toward epitope-driven vaccine development. Hum Vaccin Immunother 2014; 10,1-12; PMID,24832715; http,//dx.doi.org/10.4161/hv.29177
   PubMed Web of Science ®Google Scholar
• Mishra S, Lavelle BJ, Desrosiers J, Ardito MT, Terry F, Martin WD, De Groot AS, Gregory SH. Dendritic cell-mediated, DNA-based vaccination against hepatitis C induces the multi-epitope-specific response of humanized, HLA transgenic mice. PLoS One 2014; 9,e104606; PMID,25111185; http,//dx.doi.org/10.1371/journal.pone.0104606
   PubMedGoogle Scholar
• De Groot AS, Moise L, Liu R, Gutierrez AH, Terry F, Koita OA, Ross TM, Martin W. Cross-conservation of T-cell epitopes, now even more relevant to (H7N9) influenza vaccine design. Hum Vaccin Immunother 2014; 10,256-62; PMID,24525618; http,//dx.doi.org/10.4161/hv.28135
   PubMed Web of Science ®Google Scholar
• Liu R, Moise L, Sangare K, Desrosiers J, Martin W, De Groot AS. Immunogenicity of Teffector and Treg epitopes from H7N9 avian-origin influenza, impact of cross-reactivity with the human genome. J Immunol. 2014 May 1; 192(1) Suppl, 72.12
   Web of Science ®Google Scholar
• He L, De Groot AS, Gutierrez AH, Martin WD, Moise L, Bailey-Kellogg C. Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage. BMC Bioinformatics 2014; 15,S1; PMID,25104221; http,//dx.doi.org/10.1186/1471-2105-15-S4-S1
   PubMed Web of Science ®Google Scholar
• De Groot AS, Sbai H, Saint-Aubin C, McMurry J, Martin WD. Immuno-informatics, mining genomes for vaccine components. Immunol Cell Biol 2002; 80,255-69; PMID,12067413; http,//dx.doi.org/10.1046/j.1440-1711.2002.01092.x
   PubMed Web of Science ®Google Scholar
• De Groot AS, Martin W. Reducing risk, improving outcomes, bioengineering less immunogenic protein therapeutics. Clin Immunol 2009; 131,189-201; PMID,19269256; http,//dx.doi.org/10.1016/j.clim.2009.01.009
   PubMed Web of Science ®Google Scholar
• Sette A, Sidney J. Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics 1999, 50, 201-212
   PubMed Web of Science ®Google Scholar
• Southwood S, Sidney J, Kondo A, del Guercio MF, Appella E, Hoffman S, Kubo RT, Chesnut RW, Grey HM, Sette A, Several common HLA-DR types share largely overlapping peptide binding repertoires. J. Immunol. Baltim. Md 1950 1998, 160, 3363-3373
   Google Scholar
• Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sahin U, Braxenthaler M, Gallazzi F, Protti MP, Sinigaglia F, Hammer J. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol. 1999; 17(6),555-61; PMID,10385319; http,//dx.doi.org/10.1038/9858
   PubMed Web of Science ®Google Scholar
• Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S. Prediction of proteasome cleavage motifs by neural networks. Protein Eng 2002; 15,287-96; PMID,11983929; http,//dx.doi.org/10.1093/protein/15.4.287
   PubMedGoogle Scholar
• Zhang GL, Petrovsky N, Kwoh CK, August JT, Brusic V. PRED(TAP), a system for prediction of peptide binding to the human transporter associated with antigen processing. Immunome Res. 2006 May 23; 2,3; http,//dx.doi.org/10.1186/1745-7580-2-3
   PubMedGoogle Scholar
• Carson RT, Vignali KM, Woodland DL, Vignali DA. T cell receptor recognition of MHC class II-bound peptide flanking residues enhances immunogenicity and results in altered TCR V region usage. Immunity. 1997; 7(3),387-99; PMID,9324359; http,//dx.doi.org/10.1016/S1074-7613(00)80360-X
   PubMed Web of Science ®Google Scholar
• Le Gall S, Stamegna P, Walker BD. Portable flanking sequences modulate CTL epitope processing. J Clin Invest 2007; 117,3563-75; PMID,17975674; http,//dx.doi.org/10.1172/JCI32047
   PubMed Web of Science ®Google Scholar
• Selin LK, Nahill SR, Welsh RM. Cross-reactivities in memory cytotoxic T lymphocyte recognition of heterologous viruses. J Exp Med. 1994 Jun 1; 179(6),1933-43; http,//dx.doi.org/10.1084/jem.179.6.1933
   PubMed Web of Science ®Google Scholar
• Newell EW, Ely LK, Kruse AC, Reay PA, Rodriguez SN, Lin AE, Kuhns MS, Garcia KC, Davis MM. Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k). J Immunol. 2011 May 15; 186(10),5823-32; http,//dx.doi.org/10.4049/jimmunol.1100197
   PubMed Web of Science ®Google Scholar
• Su LF, Kidd BA, Han A, Kotzin JJ, Davis MM. Virus-specific CD4(+) memory-phenotype T cells are abundant in unexposed adults. Immunity. 2013 Feb 21; 38(2),373-83; http,//dx.doi.org/10.1016/j.immuni.2012.10.021
   PubMed Web of Science ®Google Scholar
• Nelson RW, Beisang D, Tubo NJ, Dileepan T, Wiesner DL, Nielsen K, Wüthrich M, Klein BS, Kotov DI, Spainer JA, et al. T Cell Receptor Cross-Reactivity between Similar Foreign and Self Peptides Influences Naive Cell Population Size and Autoimmunity. Immunity. 2015; 42(1):95-107; PMID,25601203
   PubMed Web of Science ®Google Scholar
• De Groot AS, Moise L, Liu R, Gutierrez AH, Tassone R, Bailey-Kellogg C, Martin W. Immune camouflage, Relevance to vaccines and human immunology. Hum Vaccin Immunother. 2014; 10(12),3570-5; PMID,25483703; http,//dx.doi.org/10.4161/hv.36134
   PubMed Web of Science ®Google Scholar
• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5; 215(3),403-10; http,//dx.doi.org/10.1016/S0022-2836(05)80360-2
   PubMed Web of Science ®Google Scholar
• Martin W, Sbai H, De Groot AS. Bioinformatics tools for identifying class I-restricted epitopes. Methods 2003; 29,289-98; PMID,19619593; http,//dx.doi.org/10.1016/S1046-2023(02)00351-1
   PubMed Web of Science ®Google Scholar
• Weber CA, Mehta PJ, Ardito M, Moise L, Martin B, De Groot AS. T cell epitope, friend or foe? Immunogenicity of biologics in context. Adv Drug Deliv Rev 2009; 30;61,965-76; http,//dx.doi.org/10.1016/j.addr.2009.07.001
   PubMed Web of Science ®Google Scholar
• Gregory SH, Mott S, Phung J, Lee J, Moise L, McMurry JA, Martin W, De Groot AS. Epitope-based vaccination against pneumonic tularemia. Vaccine 2009; 27,5299-306; PMID,19616492; http,//dx.doi.org/10.1016/j.vaccine.2009.06.101
   PubMed Web of Science ®Google Scholar
• Giles BM, Ross TM. A computationally optimized broadly reactive antigen (COBRA) based H5N1 VLP vaccine elicits broadly reactive antibodies in mice and ferrets. Vaccine. 2011; 29(16),3043-54; PMID,21320540; http,//dx.doi.org/10.1016/j.vaccine.2011.01.100
   PubMed Web of Science ®Google Scholar
• Leblanc P, Moise L, Luza C, Chantaralawan K, Lezeau L, Yuan J, Field M, Richer D, Boyle C, Martin WD, et al. VaxCelerate II, rapid development of a self-assembling vaccine for Lassa fever. Hum Vaccin Immunother. 2014; 10(10),3022-38; PMID,25483693; http,//dx.doi.org/10.4161/hv.34413
   PubMed Web of Science ®Google Scholar
• McMurry JA, Gregory SH, Moise L, Rivera D, Buus S, De Groot AS. Diversity of Francisella tularensis Schu4 antigens recognized by T lymphocytes after natural infections in humans, identification of candidate epitopes for inclusion in a rationally designed tularemia vaccine. Vaccine 2007; 25,3179-91; PMID,17291638; http,//dx.doi.org/10.1016/j.vaccine.2007.01.039
   PubMed Web of Science ®Google Scholar
• Moise L, McMurry JA, Buus S, Frey S, Martin WD, De Groot AS. In silico-accelerated identification of conserved and immunogenic variola/vaccinia T-cell epitopes. Vaccine 2009; 27,6471-9; PMID,19559119
   PubMed Web of Science ®Google Scholar
• Moise L, Buller RM, Schriewer J, Lee J, Frey SE, Weiner DB, Martin W, De Groot AS. VennVax, a DNA-prime, peptide-boost multi-T-cell epitope poxvirus vaccine, induces protective immunity against vaccinia infection by T cell response alone. Vaccine 2011; 29,501-11; PMID,21055490; http,//dx.doi.org/10.1016/j.vaccine.2010.10.064
   PubMed Web of Science ®Google Scholar
• Wullner D, Zhou L, Bramhall E, Kuck A, Goletz TJ, Swanson S, Chirmule N, Jawa V. Considerations for optimization and validation of an in vitro PBMC derived T cell assay for immunogenicity prediction of biotherapeutics. Clin Immunol 2010; 137,5-14; PMID,20708973; http,//dx.doi.org/10.1016/j.clim.2010.06.018
   PubMed Web of Science ®Google Scholar
• Leblanc PR, Yuan J, Brauns T, Gelfand JA, Poznansky MC. Accelerated vaccine development against emerging infectious diseases. Hum Vaccin Immunother 2012; 8,1010-2; PMID,22777091; http,//dx.doi.org/10.4161/hv.20805
   PubMed Web of Science ®Google Scholar
• Gao R, Cao B, Hu Y, Feng Z, Wang D, Hu W, Chen J, Jie Z, Qiu H, Xu K, et al. Human infection with a novel avian-origin influenza A (H7N9) virus. N Engl J Med 2013; 368,1888-97; PMID,23577628; http,//dx.doi.org/10.1056/NEJMoa1304459
   PubMed Web of Science ®Google Scholar
• Novartis announces positive clinical trial results for novel H7N9 vaccine. Media Release on Novartis Website. Switzerland, Basel, Novartis/Newsroom/Media Releases, 2013. Available at, http,//www.novartis.com/newsroom/media-releases/en/2013/1743124.shtml.; Last accessed 28 July 2014.
   Google Scholar
• Griffin MR, Monto AS, Belongia EA, Treanor JJ, Chen Q, Chen J, Talbot HK, Ohmit SE, Coleman LA, Lofthus G, et al. Effectiveness of non-adjuvanted pandemic influenza A vaccines for preventing pandemic influenza acute respiratory illness visits in 4 U.S. communities. PLoS One 2011; 6,e23085; PMID,21857999
   PubMed Web of Science ®Google Scholar
• Grohskopf LA, Shay DK, Shimabukuro TT, Sokolow LZ, Keitel WA, Bresee JS, Cox NJ. Prevention and control of seasonal influenza with vaccines. Recommendations of the Advisory Committee on Immunization Practices–United States, 2013–2014. Center for Disease Control Morbidity and Mortality Weekly Report 2013; 62,1-43
   PubMedGoogle Scholar
• Wong SS, Jeevan T, Kercher L, Yoon SW, Petkova AM, Crumpton JC, Franks J, Debeauchamp J, Rubrum A, Seiler P, et al. A single dose of whole inactivated H7N9 influenza vaccine confers protection from severe disease but not infection in ferrets. Vaccine 2014; 32,4571-77; PMID,24950355; http,//dx.doi.org/10.1016/j.vaccine.2014.06.016
   PubMed Web of Science ®Google Scholar
• Liu R, Moise L, Tassone R, Gutierrez AH, Terry FE, Sangare K, Ardito MT, Martin WD, De Groot AS. H7N9 T Cell Epitopes That Mimic Human Sequences Are Less Immunogenic and May Induce Treg-mediated Tolerance. Hum Vaccin Immunother 2015; 19:0; PMID, 26090577
   Web of Science ®Google Scholar
• Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui HH, Grey H, Sette A. A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol 2006; 24,817-9; PMID,16767078; http,//dx.doi.org/10.1038/nbt1215
   PubMed Web of Science ®Google Scholar
• Moise L, De Groot AS. Putting immunoinformatics to the test. Nat Biotechnol 2006; 24(7),791-2; PMID,16841062; http,//dx.doi.org/10.1038/nbt0706-791
   PubMed Web of Science ®Google Scholar
• Gilbert SC. T-cell-inducing vaccines – what's the future. Immunology 2012; 135,19-26; PMID,22044118; http,//dx.doi.org/10.1111/j.1365-2567.2011.03517.x
   PubMed Web of Science ®Google Scholar
• National Cancer Institute, Available at, http://www.cancer.gov/clinicaltrials/search.; Last accessed 01 September 2014
   Google Scholar