Journal of Biomedicine and Biotechnology
Volume 2010 (2010), Article ID 297505, 15 pages
doi:10.1155/2010/297505
Methodology Report
Vaxign: The First Web-Based Vaccine Design Program for Reverse Vaccinology and Applications for Vaccine Development
1Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
2Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
3Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
Received 2 November 2009; Accepted 6 May 2010
Academic Editor: Anne S. De Groot
Copyright © 2010 Yongqun He et al. This is an open access article distributed under the
Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Linked References
- R. Rappuoli, “Reverse vaccinology,” Current Opinion in Microbiology, vol. 3, no. 5, pp. 445–450, 2000. View at Publisher · View at Google Scholar · View at Scopus
- M. Pizza, V. Scarlato, V. Masignani, et al., “Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing,” Science, vol. 287, no. 5459, pp. 1816–1820, 2000. View at Publisher · View at Google Scholar · View at Scopus
- N. Ariel, A. Zvi, and A. Zvi, “Search for potential vaccine candidate open reading frames in the Bacillus anthracis virulence plasmid pXO1: in silico and in vitro screening,” Infection and Immunity, vol. 70, no. 12, pp. 6817–6827, 2002. View at Publisher · View at Google Scholar · View at Scopus
- B. C. Ross, L. Czajkowski, and L. Czajkowski, “Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis,” Vaccine, vol. 19, no. 30, pp. 4135–4142, 2001. View at Publisher · View at Google Scholar · View at Scopus
- S. Montigiani, F. Falugi, and F. Falugi, “Genomic approach for analysis of surface proteins in Chlamydia pneumoniae,” Infection and Immunity, vol. 70, no. 1, pp. 368–379, 2002. View at Publisher · View at Google Scholar · View at Scopus
- T. M. Wizemann, J. H. Heinrichs, and J. H. Heinrichs, “Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection,” Infection and Immunity, vol. 69, no. 3, pp. 1593–1598, 2001. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- D. N. Chakravarti, M. J. Fiske, L. D. Fletcher, and R. J. Zagursky, “Application of genomics and proteomics for identification of bacterial gene products as potential vaccine candidates,” Vaccine, vol. 19, no. 6, pp. 601–612, 2000. View at Publisher · View at Google Scholar · View at Scopus
- J. C. Betts, “Transcriptomics and proteomics: tools for the identification of novel drug targets and vaccine candidates for tuberculosis,” IUBMB Life, vol. 53, no. 4-5, pp. 239–242, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- A. S. De Groot, “Immunomics: discovering new targets for vaccines and therapeutics,” Drug Discovery Today, vol. 11, no. 5-6, pp. 203–209, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- J. L. Gardy, M. R. Laird, F. Chen, S. Rey, C. J. Walsh, M. Ester, and F. S. L. Brinkman, “PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis,” Bioinformatics, vol. 21, no. 5, pp. 617–623, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- L. Käll, A. Krogh, and E. L. Sonnhammer, “Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server,” Nucleic Acids Research, vol. 35, pp. W429–W432, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- G. Sachdeva, K. Kumar, P. Jain, and S. Ramachandran, “SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks,” Bioinformatics, vol. 21, no. 4, pp. 483–491, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- L. Li, C. J. Stoeckert Jr., and D. S. Roos, “OrthoMCL: identification of ortholog groups for eukaryotic genomes,” Genome Research, vol. 13, no. 9, pp. 2178–2189, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- S. Henikoff, J. G. Henikoff, and S. Pietrokovski, “Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations,” Bioinformatics, vol. 15, no. 6, pp. 471–479, 1999. View at Publisher · View at Google Scholar · View at Scopus
- P. A. Reche, J.-P. Glutting, H. Zhang, and E. L. Reinherz, “Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles,” Immunogenetics, vol. 56, no. 6, pp. 405–419, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- B. Peters, H. H. Bui, and H. H. Bui, “A community resource benchmarking predictions of peptide binding to MHC-I molecules,” PLoS Computational Biology, vol. 2, no. 6 , article e65, 2006. View at Publisher · View at Google Scholar · View at PubMed
- H.-G. Rammensee, J. Bachmann, N. P. N. Emmerich, O. A. Bachor, and S. Stevanović, “SYFPEITHI: database for MHC ligands and peptide motifs,” Immunogenetics, vol. 50, no. 3-4, pp. 213–219, 1999. View at Scopus
- S. Vivona, F. Bernante, and F. Filippini, “NERVE: new enhanced reverse vaccinology environment,” BMC Biotechnology, vol. 6, article 35, 2006. View at Publisher · View at Google Scholar · View at PubMed
- A. S. De Groot, H. Sbai, C. S. Aubin, J. McMurry, and W. Martin, “Immuno-informatics: mining genomes for vaccine components,” Immunology and Cell Biology, vol. 80, no. 3, pp. 255–269, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- C. DeLisi and J. A. Berzofsky, “T-cell antigenic sites tend to be amphipathic structures,” Proceedings of the National Academy of Sciences of the United States of America, vol. 82, no. 20, pp. 7048–7052, 1985. View at Scopus
- A. Sette, S. Buus, and S. Buus, “Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 9, pp. 3296–3300, 1989. View at Scopus
- O. Rotzschke, K. Falk, S. Stevanovic, G. Jung, P. Walden, and H.-G. Rammensee, “Exact prediction of a natural T cell epitope,” European Journal of Immunology, vol. 21, no. 11, pp. 2891–2894, 1991. View at Scopus
- A. Sette, J. Sidney, and J. Sidney, “HLA DR4w4-binding motifs illustrate the biochemical basis of degeneracy and specificity in peptide-DR interactions,” Journal of Immunology, vol. 151, no. 6, pp. 3163–3170, 1993. View at Scopus
- M. P. Davenport, I. A. P. H. Shon, and A. V. S. Hill, “An empirical method for the prediction of T-cell epitopes,” Immunogenetics, vol. 42, no. 5, pp. 392–397, 1995. View at Scopus
- A. S. De Groot, B. M. Jesdale, E. Szu, J. R. Schafer, R. M. Chicz, and G. Deocampo, “An interactive web site providing major histocompatibility ligand predictions: application to HIV research,” AIDS Research and Human Retroviruses, vol. 13, no. 7, pp. 529–531, 1997. View at Scopus
- V. Brusic, G. Rudy, and L. C. Harrison, “MHCPEP: a database of MHC-binding peptides,” Nucleic Acids Research, vol. 22, no. 17, pp. 3663–3665, 1994. View at Scopus
- B. Peters, J. Sidney, and J. Sidney, “The immune epitope database and analysis resource: from vision to blueprint,” PLoS Biology, vol. 3, no. 3, article e91, pp. 379–381, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- M. S. Litwin, C. S. Saigal, and C. S. Saigal, “Urologic diseases in America project: analytical methods and principal findings,” Journal of Urology, vol. 173, no. 3, pp. 933–937, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- I. Connell, W. Agace, P. Klemm, M. Schembri, S. Mårild, and C. Svanborg, “Type 1 fimbrial expression enhances Escherichia coli virulence for the urinary tract,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 18, pp. 9827–9832, 1996. View at Publisher · View at Google Scholar · View at Scopus
- S. Langermann, R. Möllby, and R. Möllby, “Vaccination with FimH adhesin protects cynomolgus monkeys from colonization and infection by uropathogenic Escherichia coli,” Journal of Infectious Diseases, vol. 181, no. 2, pp. 774–778, 2000. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- D. T. Uehling, W. J. Hopkins, J. E. Elkahwaji, D. M. Schmidt, and G. E. Leverson, “Phase 2 clinical trial of a vaginal mucosal vaccine for urinary tract infections,” Journal of Urology, vol. 170, no. 3, pp. 867–869, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- V. Kumar, N. K. Ganguly, K. Joshi, R. Mittal, K. Harjai, S. Chhibber, and S. Sharma, “Protective efficacy and immunogenicity of Escherichia coli K13 diphtheria toxoid conjugate against experimental ascending pyelonephritis,” Medical Microbiology and Immunology, vol. 194, no. 4, pp. 211–217, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- C. J. Alteri, E. C. Hagan, K. E. Sivick, S. N. Smith, and H. L. T. Mobley, “Mucosal immunization with iron receptor antigens protects against urinary tract infection,” PLoS Pathogens, vol. 5, no. 9, Article ID e1000586, 2009. View at Publisher · View at Google Scholar · View at PubMed
- J. A. Snyder, B. J. Haugen, and B. J. Haugen, “Transcriptome of uropathogenic Escherichia coli during urinary tract infection,” Infection and Immunity, vol. 72, no. 11, pp. 6373–6381, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- C. J. Alteri and H. L. T. Mobley, “Quantitative profile of the uropathogenic Escherichia coli outer membrane proteome during growth in human urine,” Infection and Immunity, vol. 75, no. 6, pp. 2679–2688, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- E. C. Hagan and H. L. T. Mobley, “Uropathogenic Escherichia coli outer membrane antigens expressed during urinary tract infection,” Infection and Immunity, vol. 75, no. 8, pp. 3941–3949, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- Z. Xiang and Y. He, “Vaxign: a web-based vaccine target design program for reverse vaccinology,” Procedia in Vaccinology, vol. 1, no. 1, pp. 23–29, 2009. View at Publisher · View at Google Scholar · View at Scopus
- H. R. Bigelow, D. S. Petrey, J. Liu, D. Przybylski, and B. Rost, “Predicting transmembrane beta-barrels in proteomes,” Nucleic Acids Research, vol. 32, no. 8, pp. 2566–2577, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- T. L. Bailey and M. Gribskov, “Combining evidence using p-values: application to sequence homology searches,” Bioinformatics, vol. 14, no. 1, pp. 48–54, 1998. View at Scopus
- J. A. Swets, “Measuring the accuracy of diagnostic systems,” Science, vol. 240, no. 4857, pp. 1285–1293, 1988. View at Scopus
- D. W. Huang, B. T. Sherman, and R. A. Lempicki, “Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources,” Nature Protocols, vol. 4, no. 1, pp. 44–57, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- K. D. Pruitt, T. Tatusova, and D. R. Maglott, “NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins,” Nucleic Acids Research, vol. 33, pp. D501–D504, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- F. R. Blattner, G. Plunkett III, and G. Plunkett, “The complete genome sequence of Escherichia coli K-12,” Science, vol. 277, no. 5331, pp. 1453–1462, 1997. View at Publisher · View at Google Scholar · View at Scopus
- C. Wilson, H. Tiwana, and A. Ebringer, “Molecular mimicry between HLA-DR alleles associated with rheumatoid arthritis and Proteus mirabilis as the aetiological basis for autoimmunity,” Microbes and Infection, vol. 2, no. 12, pp. 1489–1496, 2000. View at Publisher · View at Google Scholar · View at Scopus
- I. Nachamkin, B. M. Allos, and T. Ho, “Campylobacter species and Guillain-Barre syndrome,” Clinical Microbiology Reviews, vol. 11, no. 3, pp. 555–567, 1998. View at Scopus
- C. A. Weber, P. J. Mehta, M. Ardito, L. Moise, B. Martin, and A. S. De Groot, “T cell epitope: friend or foe? Immunogenicity of biologics in context,” Advanced Drug Delivery Reviews, vol. 61, no. 11, pp. 965–976, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- P. Naves, G. del Prado, and G. del Prado, “Correlation between virulence factors and in vitro biofilm formation by Escherichia coli strains,” Microbial Pathogenesis, vol. 45, no. 2, pp. 86–91, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- D. Serruto, R. Rappuoli, and M. Pizza, “Meningococcus B: from genome to vaccine,” in Genomics, Proteomics and Vaccines, G. Grandi, Ed., pp. 185–201, John Wiley & Sons, 2004.
- L. Durant, A. Metais, C. Soulama-Mouze, J.-M. Genevard, X. Nassif, and S. Escaich, “Identification of candidates for a subunit vaccine against extraintestinal pathogenic Escherichia coli,” Infection and Immunity, vol. 75, no. 4, pp. 1916–1925, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- A. G. Torres, P. Redford, R. A. Welch, and S. M. Payne, “TonB-dependent systems of uropathogenic Escherichia coli: aerobactin and heme transport and TonB are required for virulence in the mouse,” Infection and Immunity, vol. 69, no. 10, pp. 6179–6185, 2001. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- M. S. Walters and H. L. T. Mobley, “Identification of uropathogenic Escherichia coli surface proteins by shotgun proteomics,” Journal of Microbiological Methods, vol. 78, no. 2, pp. 131–135, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- S. Langermann, S. Palaszynski, and S. Palaszynski, “Prevention of mucosal Escherichia coli infection by FimH-adhesin-based systemic vaccination,” Science, vol. 276, no. 5312, pp. 607–611, 1997. View at Publisher · View at Google Scholar · View at Scopus
- D. Choudhury, A. Thompson, V. Stojanoff, S. Langermann, J. Pinkner, S. J. Hultgren, and S. D. Knight, “X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli,” Science, vol. 285, no. 5430, pp. 1061–1066, 1999. View at Publisher · View at Google Scholar · View at Scopus
- T. A. Russo, C. D. McFadden, U. B. Carlino-MacDonald, J. M. Beanan, R. Olson, and G. E. Wilding, “The Siderophore receptor IroN of extraintestinal pathogenic Escherichia coli is a potential vaccine candidate,” Infection and Immunity, vol. 71, no. 12, pp. 7164–7169, 2003. View at Publisher · View at Google Scholar · View at Scopus
- A. S. De Groot, L. Marcon, E. A. Bishop, D. Rivera, M. Kutzler, D. B. Weiner, and W. Martin, “HIV vaccine development by computer assisted design: the GAIA vaccine,” Vaccine, vol. 23, no. 17-18, pp. 2136–2148, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- T. Sturniolo, E. Bono, and E. Bono, “Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices,” Nature Biotechnology, vol. 17, no. 6, pp. 555–561, 1999. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
- A. Hosmalin, M. Clerici, and M. Clerici, “An epitope in human immunodeficiency virus 1 reverse transcriptase recognized by both mouse and human cytotoxic T lymphocytes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 87, no. 6, pp. 2344–2348, 1990. View at Scopus
- Z. Xiang, T. Todd, and T. Todd, “VIOLIN: vaccine investigation and online information network,” Nucleic Acids Research, vol. 36, no. 1, pp. D923–D928, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus