Immunological databases on the web

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Immunological databases on the web
Ole Lund Center for Biological Sequence
Analysis BioCentrum-DTU Technical University of
Denmark lund_at_cbs.dtu.dk
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Vaccines have been made for 36 of gt400 human
pathogens
HPV Rotavirus
Immunological Bioinformatics, The MIT press.
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Deaths from infectious diseases in the world in
2002
www.who.int/entity/whr/2004/annex/topic/en/annex_2
_en.pdf
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Pathogenic Viruses
1st column log10 of the number of deaths caused
by the pathogen per year2nd 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
humansRisk group 2 (RG2). Agents that are
associated with human disease which is rarely
serious and for which preventive or therapeutic
interventions are often availableRisk 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 AC, where
category A pathogens are considered the worst
bioterror threats4th 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
Data derived from /www.cbs.dtu.dk/databases/Dodo.
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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

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Databases Used for Vaccine Design

• Sequence databases
• General
• Sequences of proteins of the immune system
• Epitope databases
• Pathogen centered databases
• HIV
• mTB
• Malaria

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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/

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MHC Class I pathway
Figure by Eric A.J. Reits
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The binding of an immunodominant 9-mer Vaccinia
CTL epitope, HRP2 (KVDDTFYYV) to HLA-A0201.
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).
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Expression of HLA is codominant
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Polymorphism and polygeny
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The MHC gene region
http//www.ncbi.nlm.nih.gov/mhc/MHC.fcgi?cmdinit
user_id0probe_id0source_id0locus_id0locus_
group0proto_id0banner1kit_id0graphview0
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Human Leukocyte antigen (HLAMHC in humans)
polymorphism - alleles
http//www.anthonynolan.com/HIG/index.html
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Logos of HLA-A alleles
 

O Lund et al., Immunogenetics. 2004 55797-810
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Clustering of HLA alleles
 

O Lund et al., Immunogenetics. 2004 55797-810
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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?cmdin
  it

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Determination of peptide-HLA binding
Step I Folding of MHC class I molecules in
solution
b2m
Heavy chain
peptide
Step II Detection of de novo folded MHC class I
molecules by ELISA
C Sylvester-Hvid et al., Tissue Antigens. 2002
59251-8
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HLA Binding Results
KD\Pathogen Influenza Marburg Pox F.
tularensis Dengue Hantaan Lassa West Nile Yellow
Fever KDlt50 42 45 97 45 67 59 27 52 50 50ltKDlt500
63 39 42 21 44 20 21 41 52 KDgt500 87 29 38 6 30 1
1 22 29 35 in progress 9 1 1 4 6 4 12 31 33 Total
201 114 178 76 147 94 82 153 170

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

Søren Buus Lab
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ELISPOT assay

• Measure number of white blood cells that in vitro
  produce interferon-g 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
SLFNTVATL
SLFNTVATL
Two spots
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Influenza Peptides positive in ELISPOT
Mingjun Wang et al., submitted
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Peters B, et al. Immunogenetics. 2005 57326-36,
PLoS Biol. 2005 3e91.
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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/

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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

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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?dispatchlo
  adLinks
• Recent benchmark
• http//mhcbindingpredictions.immuneepitope.org/int
  ernal_allele.html

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B cell Epitope Databases

• Linear
• IEDB, Bcipep, Jenner, FIMM, BepiPred
• HIV specific database
• http//www.hiv.lanl.gov/content/immunology/ab_sear
  ch
• Conformational
• CED Conformational B cell epitopes
• http//web.kuicr.kyoto-u.ac.jp/ced/

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

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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/we
  breview.html

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Other Resources

• Gene expression data
• Localization prediction
• SignalP

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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/s
ervices/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/VD
Jsolver/ 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/
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Other Predictions at CBS

• Training matrix and neural network methods
• Training of Gibbs sampler

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Links to links

• IEDBs Links
• http//immuneepitope.org/hyperlinks.do?dispatchlo
  adLinks