Immunological databases on the web

Ole LundCenter for Biological Sequence Analysis

BioCentrum-DTUTechnical University of Denmark

lund@cbs.dtu.dk

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 2002

www.who.int/entity/whr/2004/annex/topic/en/annex_2_en.pdf

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) classificationDNA 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 intofour 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 classificationclassification 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 http://expasy.org/sprot/

• GenBank http://www.ncbi.nlm.nih.gov/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, 7052-60 (2004).

Expression of HLA is codominant

Polymorphism and polygeny

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

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

http://www.anthonynolan.com/HIG/index.html

 

Logos of HLA-A alleles

O Lund et al., Immunogenetics. 2004 55:797-810

 

Clustering of HLA alleles

O Lund et al., Immunogenetics. 2004 55:797-810

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

DevelopmentDevelopment

22mmHeavy chainHeavy chain

peptidepeptide IncubationIncubationPeptide-MHC Peptide-MHC complexcomplex

Determination of peptide-HLA binding

Step I: Folding of MHC class I molecules in solution

Step II: Detection of Step II: Detection of de novode novo folded MHC class I molecules by ELISA folded MHC class I molecules by ELISA

C Sylvester-Hvid et al., Tissue Antigens. 2002 59:251-8

HLA Binding Results

• 1215 peptides received• 1114 tested for binding • 827 (74%) bind with KD better than 500nM• 484 (43%) bind with KD better han 50 nM

KD\Pathogen Influenza Marburg Pox F. tularensis Dengue Hantaan Lassa West Nile Yellow FeverKD<50 42 45 97 45 67 59 27 52 5050<KD<500 63 39 42 21 44 20 21 41 52KD>500 87 29 38 6 30 11 22 29 35in progress 9 1 1 4 6 4 12 31 33Total 201 114 178 76 147 94 82 153 170

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

SLFNTVATL

SLFNTVATL

SLFNTVATL SLFNTVATLSLFNTVATL

Two spots

Influenza Peptides positive in ELISPOT

HLAPeptide Sequence Restriction KD (nM) + peptide - peptide + peptide - peptide

PB1591-599 VSDGGPNLY HLA-A1 6 18 ± 2 3 ± 3 12 ± 4 1 ± 1

NP44-52 CTELKLSDY HLA-A1 7 34 ± 5 4 ± 1 13 ± 4 0 ± 0

PB1166-174 FLKDVMESM HLA-A2 51 74 ± 10 11 ± 6 140 ± 36 20 ± 7

PB141-49 DTVNRTHQY HLA-A26 6 40 ± 3 20 ± 7 38 ± 5 24 ± 3

PB1540-548 GPATAQMAL HLA-B7 6 7 ± 2 2 ± 1 13 ± 2 6 ± 1

NP225-233 ILKGKFQTA HLA-B8 664 9 ± 4 1 ± 1 19 ± 7 2 ± 2

PA601-609 SVKEKDMTK HLA-B8 NB 23 ± 6 1 ± 1 119 ± 8 2 ± 1

PB1349-357 ARLGKGYMF HLA-B27 246 10 ± 6 1 ± 1 14 ± 4 1 ± 1

NP383-391 SRYWAIRTR HLA-B27 38 39 ± 6 1 ± 1 40 ± 6 2 ± 1

M1173-181 IRHENRMVL HLA-B39 13 14 ± 3 3 ± 1 84 ± 11 3 ± 1

NP199-207 RGINDRNFW HLA-B58 42 28 ± 5 1 ± 1 15 ± 6 2 ± 2

PB1347-355 KMARLGKGY HLA-B62 178 77 ± 20 3 ± 2 91 ± 8 10 ± 3

PB1566-574 TQIQTRRSF HLA-B62 88 15 ± 5 2 ± 2 21 ± 2 2 ± 0

Elispot assay1 Elispot assay2

Mingjun Wang et al., submitted

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

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/

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

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=loadLinks

• Recent benchmark:

• http://mhcbindingpredictions.immuneepitope.org/internal_allele.html

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/

MHC class II pathway

Figure by Eric A.J. Reits

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/

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.html

Other Resources

• Gene expression data

• Localization prediction

• SignalP

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 processinghttp://www.cbs.dtu.dk/services/NetChop-3.0/

B-cell epitopeshttp://www.cbs.dtu.dk/services/BepiPred/ http://www.cbs.dtu.dk/services/DiscoTope/

Plotting of epitopes relative to reference sequencehttp://www.cbs.dtu.dk/services/EpiPlot-1.0/

Analysis of human immunoglobulin VDJ recombinationhttp://www.cbs.dtu.dk/services/VDJsolver/

Geno-pheno type association based mapping of binding siteshttp://www.cbs.dtu.dk/services/SigniSite/

PhD/master course in Immunological Bioinformatics, June, 2008http://www.cbs.dtu.dk/courses/27685.imm/

Other Predictions at CBS

• Training matrix and neural network methods

• Training of Gibbs sampler

Links to links

• IEDB’s Links

• http://immuneepitope.org/hyperlinks.do?dispatch=loadLinks