Post-genomic vaccine development

FEBS Letters

Volumn 580, Issue 12, 2006, Pages 2985-2992

  Serruto, Davide ^a   Rappuoli, Rino ^a  

^a NOVARTIS VACCINES AND DIAGNOSTICS   (Italy)

Author keywords

Microarray; Pan genome; Proteomics; Reverse vaccinology; Structural biology; Vaccines

Indexed keywords

BACTERIAL VACCINE; BCG VACCINE; CHOLERA VACCINE; DIPHTHERIA TOXOID; HAEMOPHILUS INFLUENZAE VACCINE; HEPATITIS B VACCINE; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; INACTIVATED VACCINE; INFLUENZA VACCINE; LIVE VACCINE; MEASLES MUMPS RUBELLA VACCINE; MENINGOCOCCUS VACCINE; ORAL POLIOMYELITIS VACCINE; PERTUSSIS TOXIN; PNEUMOCOCCUS VACCINE; POLIOMYELITIS VACCINE; RABIES VACCINE; STREPTOCOCCUS VACCINE; TETANUS TOXOID;

BACTERIAL MEMBRANE; CHLAMYDOPHILA PNEUMONIAE; DNA MICROARRAY; DRUG DESIGN; GENE EXPRESSION; GENOME; HUMAN; IMMUNE RESPONSE; MENINGITIS; NEISSERIA MENINGITIDIS; NONHUMAN; PLASMODIUM FALCIPARUM; PORPHYROMONAS GINGIVALIS; PRIORITY JOURNAL; PROTEOMICS; SEPSIS; SHORT SURVEY; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS AGALACTIAE; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS PYOGENES; STRUCTURAL GENOMICS; VACCINE PRODUCTION;

GENOME; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOMICS; VACCINES;

EID: 33646569665     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2006.04.084     Document Type: Short Survey

References (54)

1. Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., Bult C.J., Tomb J.F., Dougherty B.A., Merrick J.M., McKenney K., Sutton G., FitzHugh W., Fields C., Gocayne J.D., Scott J., Shirley R., Liu L.-I., Glodek A., Kelley J.M., Weidman J.F., Phillips C.A., Spiggs T., Hedblom E., Cotton M.D., Utterback T.R., Hanna M.C., Nguyen D.T., Saudek D.M., Brandon R.C., Fine L.D., Fritchman J.L., Fuhrmann J.L., Geoghagen N.S.M., Gnehm C.L., McDonald L.A., Small K.V., Fraser C.M., Smith H.O., and Venter J.C. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269 (1995) 496-512
2. Fraser C.M., and Rappuoli R. Application of microbial genomic science to advanced therapeutics. Annu. Rev. Med. 56 (2005) 459-474
3. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., and Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 (2005) 376-380
4. Shendure J., Porreca G.J., Reppas N.B., Lin X., McCutcheon J.P., Rosenbaum A.M., Wang M.D., Zhang K., Mitra R.D., and Church G.M. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309 (2005) 1728-1732
5. Raskin D.M., Seshadri R., Pukatzki S.U., and Mekalanos J.J. Bacterial genomics and pathogen evolution. Cell 124 (2006) 703-714
6. Rappuoli R. Reverse vaccinology. Curr. Opin. Microbiol. 3 (2000) 445-450
7. Balmer P., and Miller E. Meningococcal disease: how to prevent and how to manage. Curr. Opin. Infect. Dis. 15 (2002) 275-281
8. Tettelin H., Saunders N.J., Heidelberg J., Jeffries A.C., Nelson K.E., Eisen J.A., Ketchum K.A., Hood D.W., Peden J.F., Dodson R.J., Nelson W.C., Gwinn M.L., DeBoy R., Peterson J.D., Hickey E.K., Haft D.H., Salzberg S.L., White O., Fleischmann R.D., Dougherty B.A., Mason T., Ciecko A., Parksey D.S., Blair E., Cittone H., Clark E.B., Cotton M.D., Utterback T.R., Khouri H., Qin H., Vamathevan J., Gill J., Scarlato V., Masignani V., Pizza M., Grandi G., Sun L., Smith H.O., Fraser C.M., Moxon E.R., Rappuoli R., and Venter J.C. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287 (2000) 1809-1815
9. Pizza M., Scarlato V., Masignani V., Giuliani M.M., Arico B., Comanducci M., Jennings G.T., Baldi L., Bartolini E., Capecchi B., Galeotti C.L., Luzzi E., Manetti R., Marchetti E., Mora M., Nuti S., Ratti G., Santini L., Savino S., Scarselli M., Storni E., Zuo P., Broeker M., Hundt E., Knapp B., Blair E., Mason T., Tettelin H., Hood D.W., Jeffries A.C., Saunders N.J., Granoff D.M., Venter J.C., Moxon E.R., Grandi G., and Rappuoli R. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287 (2000) 1816-1820
10. Schuchat A., and Wenger J.D. Epidemiology of group B streptococcal disease. Risk factors, prevention strategies, and vaccine development. Epidemiol. Rev. 16 (1994) 374-402
11. Davies H.D., Raj S., Adair C., Robinson J., and McGeer A. Population-based active surveillance for neonatal group B streptococcal infections in Alberta, Canada: implications for vaccine formulation. Pediatr. Infect. Dis. J. 20 (2001) 879-884
12. Tettelin H., Masignani V., Cieslewicz M.J., Eisen J.A., Peterson S., Wessels M.R., Paulsen I.T., Nelson K.E., Margarit I., Read T.D., Madoff L.C., Wolf A.M., Beanan M.J., Brinkac L.M., Daugherty S.C., DeBoy R.T., Durkin A.S., Kolonay J.F., Madupu R., Lewis M.R., Radune D., Fedorova N.B., Scanlan D., Khouri H., Mulligan S., Carty H.A., Cline R.T., Van Aken S.E., Gill J., Scarselli M., Mora M., Iacobini E.T., Brettoni C., Galli G., Mariani M., Vegni F., Maione D., Rinaudo D., Rappuoli R., Telford J.L., Kasper D.L., Grandi G., and Fraser C.M. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc. Natl. Acad. Sci. USA 99 (2002) 12391-12396
13. Tettelin H., Masignani V., Cieslewicz M.J., Donati C., Medini D., Ward N.L., Angiuoli S.V., Crabtree J., Jones A.L., Durkin A.S., Deboy R.T., Davidsen T.M., Mora M., Scarselli M., Margarit y Ros I., Peterson J.D., Hauser C.R., Sundaram J.P., Nelson W.C., Madupu R., Brinkac L.M., Dodson R.J., Rosovitz M.J., Sullivan S.A., Daugherty S.C., Haft D.H., Selengut J., Gwinn M.L., Zhou L., Zafar N., Khouri H., Radune D., Dimitrov G., Watkins K., O'Connor K.J., Smith S., Utterback T.R., White O., Rubens C.E., Grandi G., Madoff L.C., Kasper D.L., Telford J.L., Wessels M.R., Rappuoli R., and Fraser C.M. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc. Natl. Acad. Sci. USA 102 (2005) 13950-13955
14. Medini D., Donati C., Tettelin H., Masignani V., and Rappuoli R. The microbial pan-genome. Curr. Opin. Genet. Dev. 15 (2005) 589-594
15. Maione D., Margarit I., Rinaudo C.D., Masignani V., Mora M., Scarselli M., Tettelin H., Brettoni C., Iacobini E.T., Rosini R., D'Agostino N., Miorin L., Buccato S., Mariani M., Galli G., Nogarotto R., Nardi Dei V., Vegni F., Fraser C., Mancuso G., Teti G., Madoff L.C., Paoletti L.C., Rappuoli R., Kasper D.L., Telford J.L., and Grandi G. Identification of a universal Group B streptococcus vaccine by multiple genome screen. Science 309 (2005) 148-150
16. Brodeur B.R., Boyer M., Charlebois I., Hamel J., Couture F., Rioux C.R., and Martin D. Identification of group B streptococcal Sip protein, which elicits cross-protective immunity. Infect. Immun. 68 (2000) 5610-5618
17. Paoletti L.C., Peterson D.L., Legmann R., and Collier R.J. Preclinical evaluation of group B streptococcal polysaccharide conjugate vaccines prepared with a modified diphtheria toxin and a recombinant duck hepatitis B core antigen. Vaccine 20 (2001) 370-376
18. Lauer P., Rinaudo C.D., Soriani M., Margarit I., Maione D., Rosini R., Taddei A.R., Mora M., Rappuoli R., Grandi G., and Telford J.L. Genome analysis reveals pili in Group B Streptococcus. Science 309 (2005) 105
19. Mora M., Bensi G., Capo S., Falugi F., Zingaretti C., Manetti A.G., Maggi T., Taddei A.R., Grandi G., and Telford J.L. Group A Streptococcus produce pilus-like structures containing protective antigens and Lancefield T antigens. Proc. Natl. Acad. Sci. USA 102 (2005) 15641-15646
20. Barocchi M.A., Ries J., Zogaj X., Hemsley C., Albiger B., Kanth A., Dahlberg S., Fernebro J., Moschioni M., Masignani V., Hultenby K., Taddei A.R., Beiter K., Wartha F., von Euler A., Covacci A., Holden D.W., Normark S., Rappuoli R., and Henriques-Normark B. A pneumococcal pilus influences virulence and host inflammatory responses. Proc. Natl. Acad. Sci. USA (2006)
21. Cummings C.A., and Relman D.A. Using DNA microarrays to study host-microbe interactions. Emerg. Infect. Dis. 6 (2000) 513-525
22. Schoolnik G.K. Microarray analysis of bacterial pathogenicity. Adv. Microb. Physiol. 46 (2002) 1-45
23. Conway T., and Schoolnik G.K. Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Mol. Microbiol. 47 (2003) 879-889
24. Bryant P.A., Venter D., Robins-Browne R., and Curtis N. Chips with everything: DNA microarrays in infectious diseases. Lancet Infect. Dis. 4 (2004) 100-111
25. Rappuoli R. Pushing the limits of cellular microbiology: microarrays to study bacteria-host cell intimate contacts. Proc. Natl. Acad. Sci. USA 97 (2000) 13467-13469
26. Grifantini R., Bartolini E., Muzzi A., Draghi M., Frigimelica E., Berger J., Ratti G., Petracca R., Galli G., Agnusdei M., Giuliani M.M., Santini L., Brunelli B., Tettelin H., Rappuoli R., Randazzo F., and Grandi G. Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat. Biotechnol. 20 (2002) 914-921
27. Pandey A., and Mann M. Proteomics to study genes and genomes. Nature 405 (2000) 837-846
28. Grandi G. Antibacterial vaccine design using genomics and proteomics. Trends Biotechnol. 19 (2001) 181-188
29. Righetti P.G., Hamdan M., Reymond F., and Rossier J.L. The proteome, Anno domini Two Zero Zero Three. In: Grandi G. (Ed). Genomics Proteomics and Vaccines (2004), Wiley 103-134
30. Klade C.S. Proteomics approaches towards antigen discovery and vaccine development. Curr. Opin. Mol. Ther. 4 (2002) 216-223
31. Vytvytska O., Nagy E., Bluggel M., Meyer H.E., Kurzbauer R., Huber L.A., and Klade C.S. Identification of vaccine candidate antigens of Staphylococcus aureus by serological proteome analysis. Proteomics 2 (2002) 580-590
32. Rodriguez-Ortega M.J., Norais N., Bensi G., Liberatori S., Capo S., Mora M., Scarselli M., Doro F., Ferrari G., Garaguso I., Maggi T., Neumann A., Covre A., Telford J.L., and Grandi G. Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome. Nat. Biotechnol. 24 (2006) 191-197
33. Harrison S.C. Whither structural biology?. Nat. Struct. Mol. Biol. 11 (2004) 12-15
34. Kaldor S.W., Kalish V.J., Davies II J.F., Shetty B.V., Fritz J.E., Appelt K., Burgess J.A., Campanale K.M., Chirgadze N.Y., Clawson D.K., Dressman B.A., Hatch S.D., Khalil D.A., Kosa M.B., Lubbehusen P.P., Muesing M.A., Patick A.K., Reich S.H., Su K.S., and Tatlock J.H. Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease. J. Med. Chem. 40 (1997) 3979-3985
35. Kim C.U., Lew W., Williams M.A., Liu H., Zhang L., Swaminathan S., Bischofberger N., Chen M.S., Mendel D.B., Tai C.Y., Laver W.G., and Stevens R.C. Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity. J. Am. Chem. Soc. 119 (1997) 681-690
36. Douek D.C., Kwong P.D., and Nabel G.J. The rational design of an AIDS vaccine. Cell 124 (2006) 677-681
37. Goulding C.W., Apostol M., Anderson D.H., Gill H.S., Smith C.V., Kuo M.R., Yang J.K., Waldo G.S., Suh S.W., Chauhan R., Kale A., Bachhawat N., Mande S.C., Johnston J.M., Lott J.S., Baker E.N., Arcus V.L., Leys D., McLean K.J., Munro A.W., Berendzen J., Sharma V., Park M.S., Eisenberg D., Sacchettini J., Alber T., Rupp B., Jacobs Jr. W., and Terwilliger T.C. The TB structural genomics consortium: providing a structural foundation for drug discovery. Curr. Drug. Targets Infect. Disord. 2 (2002) 121-141
38. Rupp B. High-throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization Facility. Acc. Chem. Res. 36 (2003) 173-181
39. Smith C.V., and Sacchettini J.C. Mycobacterium tuberculosis: a model system for structural genomics. Curr. Opin. Struct. Biol. 13 (2003) 658-664
40. Belisle J.T., Vissa V.D., Sievert T., Takayama K., Brennan P.J., and Besra G.S. Role of the major antigen of Mycobacterium tuberculosis in cell wall biogenesis. Science 276 (1997) 1420-1422
41. Schorey J.S., Carroll M.C., and Brown E.J. A macrophage invasion mechanism of pathogenic mycobacteria. Science 277 (1997) 1091-1093
42. Ronning D.R., Klabunde T., Besra G.S., Vissa V.D., Belisle J.T., and Sacchettini J.C. Crystal structure of the secreted form of antigen 85C reveals potential targets for mycobacterial drugs and vaccines. Nat. Struct. Biol. 7 (2000) 141-146
43. Cantini F., Savino S., Scarselli M., Masignani V., Pizza M., Romagnoli G., Swennen E., Veggi D., Banci L., and Rappuoli R. Solution structure of the immunodominant domain of protective antigen GNA1870 of Neisseria meningitidis. J. Biol. Chem. 281 (2006) 7220-7227
44. Wizemann T.M., Heinrichs J.H., Adamou J.E., Erwin A.L., Kunsch C., Choi G.H., Barash S.C., Rosen C.A., Masure H.R., Tuomanen E., Gayle A., Brewah Y.A., Walsh W., Barren P., Lathigra R., Hanson M., Langermann S., Johnson S., and Koenig S. Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection. Infect. Immun. 69 (2001) 1593-1598
45. Hoskins J., Alborn Jr. W.E., Arnold J., Blaszczak L.C., Burgett S., DeHoff B.S., Estrem S.T., Fritz L., Fu D.J., Fuller W., Geringer C., Gilmour R., Glass J.S., Khoja H., Kraft A.R., Lagace R.E., LeBlanc D.J., Lee L.N., Lefkowitz E.J., Lu J., Matsushima P., McAhren S.M., McHenney M., McLeaster K., Mundy C.W., Nicas T.I., Norris F.H., O'Gara M., Peery R.B., Robertson G.T., Rockey P., Sun P.M., Winkler M.E., Yang Y., Young-Bellido M., Zhao G., Zook C.A., Baltz R.H., Jaskunas S.R., Rosteck Jr. P.R., Skatrud P.L., and Glass J.I. Genome of the bacterium Streptococcus pneumoniae strain R6. J. Bacteriol. 183 (2001) 5709-5717
46. Etz H., Minh D.B., Henics T., Dryla A., Winkler B., Triska C., Boyd A.P., Sollner J., Schmidt W., von Ahsen U., Buschle M., Gill S.R., Kolonay J., Khalak H., Fraser C.M., von Gabain A., Nagy E., and Meinke A. Identification of in vivo expressed vaccine candidate antigens from Staphylococcus aureus. Proc. Natl. Acad. Sci. USA 99 (2002) 6573-6578
47. Nagy E., Henics T., von Gabain A., and Meinke A. Identification of the "Antigenome" - a novel tool for design and development of subunit vaccines against bacterial pathogens. In: Grandi G. (Ed). Genomics Proteomics and Vaccines (2004), Wiley 223-244
48. Ross B.C., Czajkowski L., Hocking D., Margetts M., Webb E., Rothel L., Patterson M., Agius C., Camuglia S., Reynolds E., Littlejohn T., Gaeta B., Ng A., Kuczek E.S., Mattick J.S., Gearing D., and Barr I.G. Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis. Vaccine 19 (2001) 4135-4142
49. Hughes M.J., Moore J.C., Lane J.D., Wilson R., Pribul P.K., Younes Z.N., Dobson R.J., Everest P., Reason A.J., Redfern J.M., Greer F.M., Paxton T., Panico M., Morris H.R., Feldman R.G., and Santangelo J.D. Identification of major outer surface proteins of Streptococcus agalactiae. Infect. Immun. 70 (2002) 1254-1259
50. Reid S.D., Green N.M., Buss J.K., Lei B., and Musser J.M. Multilocus analysis of extracellular putative virulence proteins made by group A Streptococcus: population genetics, human serologic response, and gene transcription. Proc. Natl. Acad. Sci. USA 98 (2001) 7552-7557
51. Reid S.D., Green N.M., Sylva G.L., Voyich J.M., Stenseth E.T., DeLeo F.R., Palzkill T., Low D.E., Hill H.R., and Musser J.M. Postgenomic analysis of four novel antigens of group a streptococcus: growth phase-dependent gene transcription and human serologic response. J. Bacteriol. 184 (2002) 6316-6324
52. Montigiani S., Falugi F., Scarselli M., Finco O., Petracca R., Galli G., Mariani M., Manetti R., Agnusdei M., Cevenini R., Donati M., Nogarotto R., Norais N., Garaguso I., Nuti S., Saletti G., Rosa D., Ratti G., and Grandi G. Genomic approach for analysis of surface proteins in Chlamydia pneumoniae. Infect. Immun. 70 (2002) 368-379
53. Long C.A., and Hoffman S.L. Parasitology. Malaria-from infants to genomics to vaccines. Science 297 (2002) 345-347
54. Kooij T.W., Janse C.J., and Waters A.P. Plasmodium post-genomics: better the bug you know?. Nat. Rev. Microbiol. 4 (2006) 344-357