Immunological databases on the web Ole Lund Center for Biological Sequence Analysis BioCentrum-DTU Technical University of Denmark

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

Deaths from infectious diseases in the world in

Pathogenic Viruses Data derived from / 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

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

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

Sequence Databases Used to study sequence variability of microbes Sequence conservation Positive/negative selection Examples Swissprot GenBank

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

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, (2004).

Expression of HLA is codominant

Polymorphism and polygeny

The MHC gene region

Human Leukocyte antigen (HLA=MHC in humans) polymorphism - alleles

Logos of HLA-A alleles O Lund et al., Immunogenetics :

Clustering of HLA alleles O Lund et al., Immunogenetics :

Databases of Sequences of Proteins of Immune system Used to study variability of the human genome Anthony Nolan Database (IMGT/HLA sequences) IMmunoGeneTics HLA (IMGT/HLA) database Sequences of HLA, antibody and other molecules dbMHC Clinical data and sequences related to the immune system

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 :251-8

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 < <K D < K D > in progress Total Søren Buus Lab

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

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

Peters B, et al. Immunogenetics :326-36, PLoS Biol :e91.

Epitope Databases Used to find regions that can be recognized by the immune system General Epitope Databases IEDB General epitope database AntiJen (MHC Ligand, TCR-MHC Complexes, T Cell Epitope, TAP, B Cell Epitope molecules and immunological Protein-Protein interactions) FIMM (MHC, antigens, epitopes, and diseases)

More Epitope Databases SYFPEITHI Natural ligands: sequences of peptides eluded from MHC molecules on the surface of cells MHCBN: Immune related databases and predictors HLA Ligand/Motif Database: Discontinued MHCPep: Static since 1998, replaced by FIMM

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

B cell Epitope Databases Linear IEDB, Bcipep, Jenner, FIMM, BepiPred HIV specific database Conformational CED: Conformational B cell epitopes

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

Pathogen Centered Databases HIV Influenza Tuberculosis POX

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

Other Resources Gene expression data Localization prediction SignalP

Immunological resources at CBS Web servers CTL epitopes MHC binding Proteasome processing B-cell epitopes Plotting of epitopes relative to reference sequence Analysis of human immunoglobulin VDJ recombination Geno-pheno type association based mapping of binding sites PhD/master course in Immunological Bioinformatics, June,

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

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