Skip to main content
SpringerLink
Log in

Design of New Vaccines in the Genomic and Post-genomic Era

  • Chapter
  • First Online:
Innovation in Vaccinology

Abstract

During the twentieth century, the introduction of vaccines changed the history of mankind, eliminating most of the childhood diseases that used to cause millions of deaths. However, where conventional vaccinology approaches failed, many new and emerging infectious diseases remain a threat to health worldwide. The advent of whole-genome sequencing and innovation in bioinformatic tools radically changed the way to design and develop new and improved vaccines, starting from the genomic information of a single bacterial or viral isolate, with a process named reverse vaccinology. As the genomic era progressed, reverse vaccinology has evolved in combination with different approaches, such as transcriptomics, metabolomics, structural genomics, proteomics, and immunomics, contributing to the design of new and universal vaccines. Furthermore, the genomic information of the host is increasingly being used to aid understanding of the human immune response to vaccines.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Artenstein AW, Grabenstein JD (2008) Smallpox vaccines for biodefense: need and feasibility. Expert Rev Vac 7:1225–1237

    Article  Google Scholar 

  • Barocchi MA, Ries J, Zogaj X, Hemsley C, Albiger B, Kanth A, Dahlberg S, Fernebro J, Moschioni M, Masignani V, Hultenby K, Taddei AR, Beiter K, Wartha F, von Euler A, Covacci A, Holden DW, Normark S, Rappuoli R, Henriques-Normark B (2006) A pneumococcal pilus influences virulence and host inflammatory responses. Proc Natl Acad Sci USA 103:2857–2862

    Article  PubMed  CAS  Google Scholar 

  • Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21(1 Suppl):33–37

    Article  PubMed  CAS  Google Scholar 

  • Brzuszkiewicz E, Bruggemann H, Liesegang H, Emmerth M, Olschlager T, Nagy G, Albermann K, Wagner C, Buchrieser C, Emody L, Gottschalk G, Hacker J, Dobrindt U (2006) How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc Natl Acad Sci USA 103:12879–12884

    Article  PubMed  Google Scholar 

  • Buonaguro L, Pulendran B (2011) Immunogenomics and systems biology of vaccines. Immunol Rev 239:197–208

    Article  PubMed  CAS  Google Scholar 

  • Burton DR (2010) Scaffolding to build a rational vaccine design strategy. Proc Natl Acad Sci USA 107:17859–17860

    Article  PubMed  CAS  Google Scholar 

  • Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G (1999) Making and reading microarrays. Nat Genet 21(1 Suppl):15–19

    Article  PubMed  CAS  Google Scholar 

  • Davies DH, Liang X, Hernandez JE, Randall A, Hirst S, Mu Y, Romero KM, Nguyen TT, Kalantari-Dehaghi M, Crotty S, Baldi P, Villarreal LP, Felgner PL (2005) Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc Natl Acad Sci USA 102:547–552

    Article  PubMed  CAS  Google Scholar 

  • Dhiman N, Smith DI, Poland GA (2009) Next-generation sequencing: a transformative tool for vaccinology. Expert Rev Vac 8:963–967

    Article  CAS  Google Scholar 

  • Dormitzer PR, Ulmer JB, Rappuoli R (2008) Structure-based antigen design: a strategy for next generation vaccines. Trends Biotechnol 26:659–667

    Article  PubMed  CAS  Google Scholar 

  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512

    Article  PubMed  CAS  Google Scholar 

  • Giuliani MM, Adu-Bobie J, Comanducci M, Arico B, Savino S, Santini L, Brunelli B, Bambini S, Biolchi A, Capecchi B, Cartocci E, Ciucchi L, Di Marcello F, Ferlicca F, Galli B, Luzzi E, Masignani V, Serruto D, Veggi D, Contorni M, Morandi M, Bartalesi A, Cinotti V, Mannucci D, Titta F, Ovidi E, Welsch JA, Granoff D, Rappuoli R, Pizza M (2006) A universal vaccine for serogroup B meningococcus. Proc Natl Acad Sci USA 103:10834–10839

    Article  PubMed  CAS  Google Scholar 

  • Grandi G (2001) Antibacterial vaccine design using genomics and proteomics. Trends Biotechnol 19:181–188

    Article  PubMed  CAS  Google Scholar 

  • Grifantini R, Bartolini E, Muzzi A, Draghi M, Frigimelica E, Berger J, Ratti G, Petracca R, Galli G, Agnusdei M, Giuliani MM, Santini L, Brunelli B, Tettelin H, Rappuoli R, Randazzo F, Grandi G (2002) Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat Biotechnol 20:914–921

    Article  PubMed  CAS  Google Scholar 

  • Hughes MJ, Moore JC, Lane JD, Wilson R, Pribul PK, Younes ZN, Dobson RJ, Everest P, Reason AJ, Redfern JM, Greer FM, Paxton T, Panico M, Morris HR, Feldman RG, Santangelo JD (2002) Identification of major outer surface proteins of Streptococcus agalactiae. Infect Immun 70:1254–1259

    Article  PubMed  CAS  Google Scholar 

  • Hughes MJ, Wilson R, Moore JC, Lane JD, Dobson RJ, Muckett P, Younes Z, Pribul P, Topping A, Feldman RG, Santangelo JD (2003) Novel protein vaccine candidates against Group B streptococcal infection identified using alkaline phosphatase fusions. FEMS Microbiol Lett 222(2):263–271

    Article  PubMed  CAS  Google Scholar 

  • Kaushik DK, Sehgal D (2008) Developing antibacterial vaccines in genomics and proteomics era. Scand J Immunol 67:544–552

    Article  PubMed  CAS  Google Scholar 

  • Kelly D, Moxon ER (2004) Is Haemophilus influenzae type b disease finished? Adv Exp Med Biol 549:221–229

    Article  PubMed  Google Scholar 

  • Langen H, Takacs B, Evers S, Berndt P, Lahm HW, Wipf B, Gray C, Fountoulakis M (2000) Two-dimensional map of the proteome of Haemophilus influenzae. Electrophoresis 21:411–429

    Article  PubMed  CAS  Google Scholar 

  • Lauer P, Rinaudo CD, Soriani M, Margarit I, Maione D, Rosini R, Taddei AR, Mora M, Rappuoli R, Grandi G, Telford JL (2005) Genome analysis reveals pili in Group B Streptococcus. Science 309:105

    Article  PubMed  CAS  Google Scholar 

  • Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nat Genet 21(1 Suppl):20–24

    Article  PubMed  CAS  Google Scholar 

  • Lockhart DJ, Winzeler EA (2000) Genomics, gene expression and DNA arrays. Nature 405:827–836

    Article  PubMed  CAS  Google Scholar 

  • Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, Scarselli M, Tettelin H, Brettoni C, Iacobini ET, Rosini R, D’Agostino N, Miorin L, Buccato S, Mariani M, Galli G, Nogarotto R, Dei VN, Vegni F, Fraser C, Mancuso G, Teti G, Madoff LC, Paoletti LC, Rappuoli R, Kasper DL, Telford JL, Grandi G (2005) Identification of a universal Group B streptococcus vaccine by multiple genome screen. Science 309:148–150

    Article  PubMed  CAS  Google Scholar 

  • Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15:589–594

    Article  PubMed  CAS  Google Scholar 

  • 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, Grandi G (2002) Genomic approach for analysis of surface proteins in Chlamydia pneumoniae. Infect Immun 70:368–379

    Article  PubMed  CAS  Google Scholar 

  • Mora M, Bensi G, Capo S, Falugi F, Zingaretti C, Manetti AG, Maggi T, Taddei AR, Grandi G, Telford JL (2005) Group A Streptococcus produce pilus-like structures containing protective antigens and Lancefield T antigens. Proc Natl Acad Sci USA 102:15641–15646

    Article  PubMed  CAS  Google Scholar 

  • Moriel DG, Bertoldi I, Spagnuolo A, Marchi S, Rosini R, Nesta B, Pastorello I, Corea VA, Torricelli G, Cartocci E, Savino S, Scarselli M, Dobrindt U, Hacker J, Tettelin H, Tallon LJ, Sullivan S, Wieler LH, Ewers C, Pickard D, Dougan G, Fontana MR, Rappuoli R, Pizza M, Serino L (2010) Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli. Proc Natl Acad Sci USA 107:9072–9077

    Article  PubMed  CAS  Google Scholar 

  • Nuccitelli A, Cozzi R, Gourlay LJ, Donnarumma D, Necchi F, Norais N, Telford JL, Rappuoli R, Bolognesi M, Maione D, Grandi G, Rinaudo CD (2011) Structure-based approach to rationally design a chimeric protein for an effective vaccine against Group B Streptococcus infections. Proc Natl Acad Sci USA 108:10278–10283

    Article  PubMed  CAS  Google Scholar 

  • Pizza M, Scarlato V, Masignani V, Giuliani MM, Arico B, Comanducci M, Jennings GT, Baldi L, Bartolini E, Capecchi B, Galeotti CL, 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 DW, Jeffries AC, Saunders NJ, Granoff DM, Venter JC, Moxon ER, Grandi G, Rappuoli R (2000) Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287:1816–1820

    Article  PubMed  CAS  Google Scholar 

  • Plotkin SA (2003) Vaccines, vaccination, and vaccinology. J Infect Dis 187:1349–1359

    Article  PubMed  CAS  Google Scholar 

  • Plotkin SA (2009) Vaccines: the fourth century. Clin Vac Immunol 16:1709–1719

    Article  CAS  Google Scholar 

  • Purcell AW, McCluskey J, Rossjohn J (2007) More than one reason to rethink the use of peptides in vaccine design. Nat Rev Drug Discov 6:404–414

    Article  PubMed  CAS  Google Scholar 

  • Qi SY, Moir A, O’Connor CD (1996) Proteome of Salmonella typhimurium SL1344: identification of novel abundant cell envelope proteins and assignment to a two-dimensional reference map. J Bacteriol 178:5032–5038

    PubMed  CAS  Google Scholar 

  • Rappuoli R (2000) Reverse vaccinology. Curr Opin Microbiol 3:445–450

    Article  PubMed  CAS  Google Scholar 

  • Rodriguez-Ortega MJ, 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 JL, Grandi G (2006) Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome. Nat Biotechnol 24:191–197

    Article  PubMed  CAS  Google Scholar 

  • Scarselli M, Arico B, Brunelli B, Savino S, Di Marcello F, Palumbo E, Veggi D, Ciucchi L, Cartocci E, Bottomley MJ, Malito E, Lo Surdo P, Comanducci M, Giuliani MM, Cantini F, Dragonetti S, Colaprico A, Doro F, Giannetti P, Pallaoro M, Brogioni B, Tontini M, Hilleringmann M, Nardi-Dei V, Banci L, Pizza M, Rappuoli R (2011) Rational design of a meningococcal antigen inducing broad protective immunity. Sci Transl Med 3:91ra62

    Article  PubMed  CAS  Google Scholar 

  • Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermuller J, Reinhardt R, Stadler PF, Vogel J (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250–255

    Article  PubMed  CAS  Google Scholar 

  • Sorek R, Cossart P (2010) Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 11:9–16

    Article  PubMed  CAS  Google Scholar 

  • Stacy R, Begley DW, Phan I, Staker BL, Van Voorhis WC, Varani G, Buchko GW, Stewart LJ, Myler PJ (2011) Structural genomics of infectious disease drug targets: the SSGCID. Acta Crystallogr Sect F Struct Biol Cryst Commun 67(Pt 9):979–984

    Article  PubMed  Google Scholar 

  • Sundaresh S, Randall A, Unal B, Petersen JM, Belisle JT, Hartley MG, Duffield M, Titball RW, Davies DH, Felgner PL, Baldi P (2007) From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. Bioinformatics 23:i508–i518

    Article  PubMed  CAS  Google Scholar 

  • Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I, Read TD, Madoff LC, Wolf AM, Beanan MJ, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Lewis MR, Radune D, Fedorova NB, Scanlan D, Khouri H, Mulligan S, Carty HA, Cline RT, Van Aken SE, Gill J, Scarselli M, Mora M, Iacobini ET, Brettoni C, Galli G, Mariani M, Vegni F, Maione D, Rinaudo D, Rappuoli R, Telford JL, Kasper DL, Grandi G, Fraser CM (2002) Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci USA 99:12391–12396

    Article  PubMed  CAS  Google Scholar 

  • Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O’Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci USA 102:13950–13955

    Article  PubMed  CAS  Google Scholar 

  • Thoren K, Gustafsson E, Clevnert A, Larsson T, Bergstrom J, Nilsson CL (2002) Proteomic study of non-typable Haemophilus influenzae. J Chromatogr B Analyt Technol Biomed Life Sci 782:219–226

    Article  PubMed  CAS  Google Scholar 

  • Tobin GJ, Trujillo JD, Bushnell RV, Lin G, Chaudhuri AR, Long J, Barrera J, Pena L, Grubman MJ, Nara PL (2008) Deceptive imprinting and immune refocusing in vaccine design. Vaccine 26:6189–6199

    Article  PubMed  CAS  Google Scholar 

  • Toneatto D, Ismaili S, Ypma E, Vienken K, Oster P, Dull P (2011) The first use of an investigational multicomponent meningococcal serogroup B vaccine (4CMenB) in humans. Hum Vaccin 7:646–653

    Article  PubMed  Google Scholar 

  • Vytvytska O, Nagy E, Bluggel M, Meyer HE, Kurzbauer R, Huber LA, Klade CS (2002) Identification of vaccine candidate antigens of staphylococcus aureus by serological proteome analysis. Proteomics 2:580–590

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Research Centre, Novartis Vaccines and Diagnostics, Via Fiorentina, 1, Siena, Italy

    Laura Serino, Kate L. Seib & Mariagrazia Pizza

Authors
  1. Laura Serino
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kate L. Seib
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mariagrazia Pizza
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mariagrazia Pizza .

Editor information

Editors and Affiliations

  1. Italian National Agency for New Technolo, Energy and Sustainable Economic Developm, ENEA, Via Anguillarese 301, Rome, 00123, Italy

    Selene Baschieri

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Serino, L., Seib, K.L., Pizza, M. (2012). Design of New Vaccines in the Genomic and Post-genomic Era. In: Baschieri, S. (eds) Innovation in Vaccinology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4543-8_1

Download citation

Publish with us

Policies and ethics

Search

Navigation