1. Immunological databases on the web Ole Lund Center for Biological Sequence Analysis BioCentrum-DTU Technical University of Denmark lund@cbs.dtu.dk

2. Vaccines have been made for 36 of >400 human pathogens Immunological Bioinformatics, The MIT press. +HPV & Rotavirus

3. Deaths from infectious diseases in the world in 2002 www.who.int/entity/whr/2004/annex/topic/en/annex_2_en.pdf

4. Pathogenic Viruses Data derived from /www.cbs.dtu.dk/databases/Dodo. 1st column: log10 of the number of deaths caused by the pathogen per year 2nd column: DNA Advisory Committee (RAC) classification DNA Advisory Committee guidelines [RAC, 2002] which includes those biological agents known to infect humans, as well as selected animal agents that may pose theoretical risks if inoculated into humans. RAC divides pathogens into four classes. Risk group 1 (RG1). Agents that are not associated with disease in healthy adult humans Risk group 2 (RG2). Agents that are associated with human disease which is rarely serious and for which preventive or therapeutic interventions are often available Risk group 3 (RG3). Agents that are associated with serious or lethal human disease for which preventive or therapeutic interventions may be available (high individual risk but low community risk) Risk group 4 (RG4). Agents that are likely to cause serious or lethal human disease for which preventive or therapeutic interventions are not usually available (high individual risk and high community risk) 3rd column: CDC/NIAID bioterror classification classification of the pathogens according to the Centers for Disease Control and Prevention (CDC) bioterror categories A–C, where category A pathogens are considered the worst bioterror threats 4th column: Vaccines available A letter indicating the type of vaccine if one is available (A: acellular/adsorbet; C: conjugate; I: inactivated; L: live; P: polysaccharide; R: recombinant; S staphage lysate; T: toxoid). Lower case indicates that the vaccine is released as an investigational new drug (IND)). 5th column: G: Complete genome is sequenced

5. Need for new vaccine technologies The classical way of making vaccines have in many cases been tried for the pathogens for which no vaccines exist Need for new ways for making vaccines

6. Databases Used for Vaccine Design Sequence databases General Sequences of proteins of the immune system Epitope databases Pathogen centered databases HIV mTB Malaria

7. Sequence Databases Used to study sequence variability of microbes Sequence conservation Positive/negative selection Examples Swissprot http://expasy.org/sprot/http://expasy.org/sprot/ GenBank http://www.ncbi.nlm.nih.gov/Genbank/http://www.ncbi.nlm.nih.gov/Genbank/

8. MHC Class I pathway Figure by Eric A.J. Reits

9. The binding of an immunodominant 9-mer Vaccinia CTL epitope, HRP2 (KVDDTFYYV) to HLA-A*0201. Position 2 and 9 of the epitopes are buried deeply in the HLA class I molecule. Figure by Anne Mølgaard, peptide (KVDDTFYYV) used as vaccine by Snyder et al. J Virol 78, 7052-60 (2004).

10. Expression of HLA is codominant

11. Polymorphism and polygeny

12. The MHC gene region http://www.ncbi.nlm.nih.gov/mhc/MHC.fcgi?cmd=init&user_id=0&probe_id=0&source_id=0&locus_id=0&locus_group=0&proto_id=0&banner=1&kit_id=0&graphview=0

13. Human Leukocyte antigen (HLA=MHC in humans) polymorphism - alleles http://www.anthonynolan.com/HIG/index.html

14. Logos of HLA-A alleles O Lund et al., Immunogenetics. 2004 55:797-810

15. Clustering of HLA alleles O Lund et al., Immunogenetics. 2004 55:797-810

16. Databases of Sequences of Proteins of Immune system Used to study variability of the human genome Anthony Nolan Database (IMGT/HLA sequences) http://www.anthonynolan.com/HIG/ IMmunoGeneTics HLA (IMGT/HLA) database Sequences of HLA, antibody and other molecules http://imgt.cines.fr/ dbMHC Clinical data and sequences related to the immune system http://www.ncbi.nlm.nih.gov/gv/mhc/main.cgi?cmd=init

17. Development 2m2m2m2m Heavy chain peptide Incubation Peptide-MHC complex Determination of peptide-HLA binding Step I: Folding of MHC class I molecules in solution Step II: Detection of de novo folded MHC class I molecules by ELISA C Sylvester-Hvid et al., Tissue Antigens. 2002 59:251-8

18. HLA Binding Results 1215 peptides received 1114 tested for binding 827 (74%) bind with K D better than 500nM 484 (43%) bind with K D better han 50 nM KD\PathogenInfluenzaMarburgPoxF. tularensisDengueHantaanLassaWest NileYellow Fever K D <50424597456759275250 50<K D <500 633942214420214152 K D >50087293863011222935 in progress911464123133 Total201114178761479482153170 Søren Buus Lab

19. ELISPOT assay Measure number of white blood cells that in vitro produce interferon-  in response to a peptide A positive result means that the immune system has earlier reacted to the peptide (during a response to a vaccine/natural infection) SLFNTVATL Two spots

20. Influenza Peptides positive in ELISPOT Mingjun Wang et al., submitted

21. Peters B, et al. Immunogenetics. 2005 57:326-36, PLoS Biol. 2005 3:e91.

22. Epitope Databases Used to find regions that can be recognized by the immune system General Epitope Databases IEDB General epitope database http://immuneepitope.org/home.do AntiJen (MHC Ligand, TCR-MHC Complexes, T Cell Epitope, TAP, B Cell Epitope molecules and immunological Protein-Protein interactions) http://www.jenner.ac.uk/AntiJen/ FIMM (MHC, antigens, epitopes, and diseases) http://research.i2r.a-star.edu.sg/fimm/

23. More Epitope Databases SYFPEITHI Natural ligands: sequences of peptides eluded from MHC molecules on the surface of cells http://www.syfpeithi.de/ MHCBN: Immune related databases and predictors http://www.imtech.res.in/raghava/mhcbn/ http://bioinformatics.uams.edu/mirror/mhcbn/ HLA Ligand/Motif Database: Discontinued MHCPep: Static since 1998, replaced by FIMM

24. Prediction of HLA binding Many methods available, including: bimas, syfpeithi, Hlaligand, libscore, mapppB, mapppS,mhcpred, netmhc, pepdist, predbalbc, predep, rankpep, svmhc See links at: http://immuneepitope.org/hyperlinks.do?dispatch=load Linkshttp://immuneepitope.org/hyperlinks.do?dispatch=load Links Recent benchmark: http://mhcbindingpredictions.immuneepitope.org/intern al_allele.htmlhttp://mhcbindingpredictions.immuneepitope.org/intern al_allele.html

25. B cell Epitope Databases Linear IEDB, Bcipep, Jenner, FIMM, BepiPred HIV specific database http://www.hiv.lanl.gov/content/immunology/ab_search Conformational CED: Conformational B cell epitopes http://web.kuicr.kyoto-u.ac.jp/~ced/

26. MHC class II pathway Figure by Eric A.J. Reits

27. Pathogen Centered Databases HIV http://www.hiv.lanl.gov/content/index Influenza http://www.flu.lanl.gov/ Tuberculosis http://www.sanger.ac.uk/Projects/M_tuberculosis/ POX http://www.poxvirus.org/

28. Reviews Tong JC, Tan TW, Ranganathan S. Methods and protocols for prediction of immunogenic epitopes. Brief Bioinform. 2006 Oct 31 Web based Tools for Vaccine Design (Lund et al, 2002) http://www.cbs.dtu.dk/researchgroups/immunology/ webreview.htmlhttp://www.cbs.dtu.dk/researchgroups/immunology/ webreview.html

29. Other Resources Gene expression data Localization prediction SignalP

30. Immunological resources at CBS Web servers CTL epitopes http://www.cbs.dtu.dk/services/NetCTL/ MHC binding http://www.cbs.dtu.dk/services/NetMHC/ http://www.cbs.dtu.dk/services/NetMHCII/ http://www.cbs.dtu.dk/services/NetMHCpan/ Proteasome processing http://www.cbs.dtu.dk/services/NetChop-3.0/ B-cell epitopes http://www.cbs.dtu.dk/services/BepiPred/ http://www.cbs.dtu.dk/services/DiscoTope/ Plotting of epitopes relative to reference sequence http://www.cbs.dtu.dk/services/EpiPlot-1.0/ Analysis of human immunoglobulin VDJ recombination http://www.cbs.dtu.dk/services/VDJsolver/ Geno-pheno type association based mapping of binding sites http://www.cbs.dtu.dk/services/SigniSite/ PhD/master course in Immunological Bioinformatics, June, 2008 http://www.cbs.dtu.dk/courses/27685.imm/

31. Other Predictions at CBS Training matrix and neural network methods Training of Gibbs sampler

32. Links to links IEDB’s Links http://immuneepitope.org/hyperlinks.do?dispatch=load Linkshttp://immuneepitope.org/hyperlinks.do?dispatch=load Links