1. Vaccines

2. Vaccination Administration of a substance to a person with the purpose of preventing a disease Traditionally composed of a killed or weakened microorganism Vaccination works by creating a type of immune response that enables the memory cells to later respond to a similar organism before it can cause disease

3. Early History of Vaccination Pioneered India and China in the 17th century The tradition of vaccination may have originated in India in AD 1000 Powdered scabs from people infected with smallpox was used to protect against the disease Smallpox was responsible for 8 to 20% of all deaths in several European countries in the 18th century In 1721 Lady Mary Wortley Montagu brought the knowledge of these techniques from Constantinople (now Istanbul) to England Two to three percent of the smallpox vaccinees, however, died from the vaccination itself Benjamin Jesty and, later, Edward Jenner could show that vaccination with the less dangerous cowpox could protect against infection with smallpox The word vaccination, which is derived from vacca, the Latin word for cow.

4. Early History of Vaccination II In 1879 Louis Pasteur showed that chicken cholera weakened by growing it in the laboratory could protect against infection with more virulent strains 1881 he showed in a public experiment at Pouilly-Le-Fort that his anthrax vaccine was efficient in protecting sheep, a goat, and cows. In 1885 Pasteur developed a vaccine against rabies based on a live attenuated virus A year later Edmund Salmon and Theobald Smith developed a (heat) killed cholera vaccine. Over the next 20 years killed typhoid and plague vaccines were developed In 1927 the bacille Calmette-Guérin (BCG vaccine) against tuberculosis vere developed

5. Vaccination since WW II Cell cultures Ability to grow cells from higher organisms such as vertebrates in the laboratory Easier to develop new vaccines The number of pathogens for which vaccines can be made have almost doubled. Many vaccines were grown in chicken embryo cells (from eggs), and even today many vaccines such as the influenza vaccine, are still produced in eggs Alternatives are being investigated

6. Vaccination Today Vaccines have been made for only 34 of the more than 400 known pathogens that are harmful to man. Immunization saves the lives of 3 million children each year, but that 2 million more lives could be saved if existing vaccines were applied on a full-scale worldwide

7. Human Vaccines against pathogens Immunological Bioinformatics, The MIT press.

8. Categories of Vaccines Live vaccines Are able to replicate in the host Attenuated (weakened) so they do not cause disease Subunit vaccines Part of organism Genetic Vaccines Part of genes from organism

9. Live Vaccines Characteristics Able to replicate in the host Attenuated (weakened) so they do not cause disease Advantages Induce a broad immune response (cellular and humoral) Low doses of vaccine are normally sufficient Long-lasting protection are often induced Disadvantages May cause adverse reactions May be transmitted from person to person

10. Subunit Vaccines Relatively easy to produce (not live) Induce little CTL Viral and bacterial proteins are not produced within cells Classically produced by inactivating a whole virus or bacterium Heat Chemicals The vaccine may be purified Selecting one or a few proteins which confer protection Bordetella pertussis (whooping cough) Create a better-tolerated vaccine that is free from whole microorganism cells

11. Subunit Vaccines: Polysaccharides Polysaccharides Many bacteria have polysaccharides in their outer membrane Polysaccharide based vaccines Neisseria meningitidis Streptococcus pneumoniae Generate a T cell-independent response Inefficient in children younger than 2 years old Overcome by conjugating the polysaccharides to peptides Used in vaccines against Streptococcus pneumoniae and Haemophilus influenzae.

12. Subunit Vaccines: Toxoids Toxins Responsible for the pathogenesis of many bacteria Toxoids Inactivated toxins Toxoid based vaccines Bordetella pertussis Clostridium tetani Corynebacterium diphtheriae Inactivation Traditionally done by chemical means Altering the DNA sequences important to toxicity

13. Subunit Vaccines: Recombinant The hepatitis B virus (HBV) vaccine Originally based on the surface antigen purified from the blood of chronically infected individuals. Due to safety concerns, the HBV vaccine became the first to be produced using recombinant DNA technology (1986) Produced in bakers’ yeast (Saccharomyces cerevisiae) Virus-like particles (VLPs) Viral proteins that self-assemble to particles with the same size as the native virus. VLP is the basis of a promising new vaccine against human papilloma virus (HPV) Merck In phase III For more information se: http://www.nci.nih.gov/ncicancerbulletin/NCI_Cancer_Bulletin_041205/page5http://www.nci.nih.gov/ncicancerbulletin/NCI_Cancer_Bulletin_041205/page5

14. Genetic Vaccines Introduce DNA or RNA into the host Injected (Naked) Coated on gold particles Carried by viruses vaccinia, adenovirus, or alphaviruses bacteria such as Salmonella typhi, Mycobacterium tuberculosis Advantages Easy to produce Induce cellular response Disadvantages Low response in 1st generation

15. Epitope based vaccines Advantages( Ishioka et al. [1999]) : Can be more potent Can be controlled better Can induce subdominant epitopes (e.g. against tumor antigens where there is tolerance against dominant epitopes) Can target multiple conserved epitopes in rapidly mutating pathogens like HIV and Hepatitis C virus (HCV) Can be designed to break tolerance Can overcome safety concerns associated with entire organisms or proteins Epitope-based vaccines have been shown to confer protection in animal models ([Snyder et al., 2004], Rodriguez et al. [1998] and Sette and Sidney [1999])

16. Passive Immunization Antibodies harvested from infected patients or animals are then used to protect against disease [Marshall et al., 2003] Used in special cases against many pathogens: Cytomegalovirus Hepatitis A and B viruses Measles Varicella Rubella Respiratory syncytial virus Rabies Clostridium tetani Varicella-zoster virus Vaccinia Clostridium botulinum Corynebacterium diphtheriae

17. Polytope optimization Successful immunization can be obtained only if the epitopes encoded by the polytope are correctly processed and presented. Cleavage by the proteasome in the cytosol, translocation into the ER by the TAP complex, as well as binding to MHC class I should be taken into account in an integrative manner. The design of a polytope can be done in an effective way by modifying the sequential order of the different epitopes, and by inserting specific amino acids that will favor optimal cleavage and transport by the TAP complex, as linkers between the epitopes.

18. Polytope starting configuration Immunological Bioinformatics, The MIT press.

19. Polytope optimization Algorithm Optimization of of four measures: 1.The number of poor C-terminal cleavage sites of epitopes (predicted cleavage < 0.9) 2.The number of internal cleavage sites (within epitope cleavages with a prediction larger than the predicted C-terminal cleavage) 3.The number of new epitopes (number of processed and presented epitopes in the fusing regions spanning the epitopes) 4.The length of the linker region inserted between epitopes. The optimization seeks to minimize the above four terms by use of Monte Carlo Metropolis simulations [Metropolis et al., 1953]

20. Polytope final configuation Immunological Bioinformatics, The MIT press.

21. Therapeutic vaccines Vaccines to treat the patients that already have a disease Targets Tumors AIDS Allergies Autoimmune diseases Hepatitis B Tuberculosis Malaria Helicobacter pylori Concept suppress/boost existing immunity or induce immune responses.

22. Cancer vaccines Break the tolerance of the immune system against tumors 3 types 1.Whole tumor cells, peptides derived from tumor cells in vitro, or heat shock proteins prepared from autologous tumor cells 2.Tumor-specific antigen–defined vaccines 3.Vaccines aiming to increase the amount of dendritic cells (DCs) that can initiate a long-lasting T cell response against tumors. Therapeutic cancer vaccines can induce antitumor immune responses in humans with cancer Antigenic variation is a major problem that therapeutic vaccines against cancer face Tools from genomics and bioinformatics may circumvent these problems Se also: http://cis.nci.nih.gov/fact/7_2.htmhttp://cis.nci.nih.gov/fact/7_2.htm

23. Allergy vaccines Increasing occurrence of allergies in industrialized countries The traditional approach is to vaccinate with small doses of purified allergen Second-generation vaccines are under development based on recombinant technology Genetically engineered Bet v 1 vaccine can reduce pollen-specific IgE memory response significantly Example of switching a “wrong” immune response to a less harmful one. Figure by Thomas Blicher.

24. Therapeutic Vaccines against Persistent Infections For example for preventing HIV-related disease progression Most of the first candidate HIV-1 vaccines were based entirely or partially on envelope proteins to boost neutralizing antibodies Envelope proteins are the most variable parts of the HIV genome Vaccines composed of monomeric gp120 molecules induce antibodies that do not bind to trimeric gp120 on the surface of virions A number of recent vaccines are also designed to induce strong cell- mediated responses. Escapes from CTL responses are associated with disease progression and high viral loads Some CTL epitopes escape recognition quickly because they are not functionally constrained, others might need several compensatory mutations because they are in functionally or structurally constrained regions of HIV-1

25. Vaccines Against Autoimmune Diseases Multiple sclerosis T cells specific for mylein basic protein (MBP) can cause inflammation of the central nervous system. The vaccine uses copolymer 1 (cop 1), a protein that highly resembles MBP. Cop 1 competes with MBP in binding to MHC class II molecules, but it is not effective in inducing a T cell response On the contrary, cop 1 can induce a suppressor T cell response specific for MBP, and this response helps diminish the symptoms of multiple sclerosis A vaccine based on the same mechanisms is developed for myasthenia gravis More information: http://www.ninds.nih.gov/disorders/multiple_sclerosis/detail_multiple_sclerosis.htm, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12667659&query_hl=4 http://www.ninds.nih.gov/disorders/multiple_sclerosis/detail_multiple_sclerosis.htm http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12667659&query_hl=4

26. Vaccines Market The vaccine market has increased fivefold from 1990 to 2000 Annual sales of 6 billion euros Less than 2% of the total pharma market. Major producers (85% of the market) GlaxoSmithKline (GSK), Merck, Aventis Pasteur, Wyeth, Chiron Main products (>50% of the market) Hepatitis B, flu, MMR (measles, mumps, and rubella) and DTP (diphtheria, tetanus, pertussis) 40% are produced in the United States and the rest is evenly split between Europe and the rest of the world [Gréco, 2002] It currently costs between 200 and 500 million US dollars to bring a new vaccine from the concept stage to market [André, 2002] More information: Gréco, 2002 André, 2002 Gréco, 2002 André, 2002

27. Trends From Whole live and killed organisms Problems Adverse effects Production To Subunit vaccines Genetic vaccines Challenges Enhance immunogenecity

28. Prediction of antigens Protective antigens Functional definition (phenotype) Which antigens will be protective (genotype)? They must be recognized by the immune system Predict epitopes (include processing) CTL (MHC class I) http://www.cbs.dtu.dk/services/NetCTL/ Helper (MHC class II) http://mail1.imtech.res.in/raghava/hlapred/index.html Antibody http://www.cbs.dtu.dk/services/BepiPred/ More Links: http://www.cbs.dtu.dk/researchgroups/immunology/webreview.html

29. Function and conservation Some of the epitopes must exist in the wild type Conservation http://www.ncbi.nlm.nih.gov/BLAST/ Function When is it expressed? Where is it trafficked to? SecretomeP Non-classical and leaderless secretion of eukaryotic proteins. SignalP Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences. TargetP Subcellular location of proteins: mitochondrial, chloroplastic, secretory pathway, or other.SecretomeP SignalP TargetP Expression level?

30. Selection of antigens Epitopes Polytope Proteins Helper epitopes Does it contain any Can they be added Hide epitopes Immunodominant and variable ones

31. NIH project PathogenHLA bindingElispot InfluenzaXX Variola major (smallpox) vaccine strainXX Yersinia pestisX Francisella tularensis (tularemia)X LCMX Lassa FeverX Hantaan virus (Korean hemorrhagic fever virus)X Rift Valley FeverX DengueX EbolaX MarburgX Multi-drug resistant TB (BCG vaccine)XX Yellow feverX Typhus fever (Rickettsia prowazekii)X West Nile VirusX Description of whole project: http://www.cbs.dtu.dk/researchgroups/immunology/EpitopeDiscovery/ http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030091 http://www.cbs.dtu.dk/researchgroups/immunology/EpitopeDiscovery/ http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030091

32. Acknowledgements Immunological Bioinformatics group, CBS, Technical University of Denmark (www.cbs.dtu.dk) Morten Nielsen HLA binding Claus Lundegaard Data bases, HLA binding Anne Mølgaard MHC binding Mette Voldby Larsen CTL prediction Pernille Haste Andersen B cell epitopes Sune Frankild Databases Jens Pontoppidan Linear B cell epitopes Collaborators IMMI, University of Copenhagen Søren BuusMHC binding Mogens H ClaessonCTL La Jolla Institute of Allergy and Infectious Diseases Allesandro SetteEpitope DB Leiden University Medical Center Tom Ottenhoff Tuberculosis Michel Klein Ganymed Ugur SahinGenetic library University of Tubingen Stefan Stevanovic MHC ligands INSERM Peter van EndertTap University of Mainz Hansjörg Schild Proteasome Schafer-Nielsen Claus Schafer-NielsenPeptides