Immunological Bioinformatics

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Immunological Bioinformatics

• Processing, combined predictions, and rational
  epitope selection

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Cellular Immunity
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Proteasome specificity

• Low polymorphism
• Constitutive Immuno-proteasome
• Evolutionary conserved
• Stochastic and low specificity
• Only 70-80 of the cleavage sites are reproduced
  in repeated experiments

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Proteasome evolution (b1 unit)
Human (Hs) - Human Drosophila (Dm) - Fly Bos
Taurus (Bota) - Cow Oncorhynchus mykiss (Om) -
Fish
Constitutive
Immuno
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Immuno- and Constitutive proteasome specificity
Immuno
Constitutive
P1
P1
...LVGPTPVNIIGRNMLTQL..
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Predicting proteasomal cleavage

• NetChop
• Neural network based method
• PaProc
• Weight matrix based method
• FragPredict
• Based on a statistical analysis of
  cleavage-determining amino acid motifs present
  around the scissile bond
• i.e. also weight matrix like

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NetChop 3.0 Cterm (MHC ligands)

• NetChop-3.0 C-term
• Trained on class I epitopes
• Most epitopes are generated by the immuno
  proteasome
• Predicts the immuno proteasome specificity

LDFVRFMGVMSSCNNPA LVQEKYLEYRQVPDSDP
RTQDENPVVHFFKNIVT TPLIPLTIFVGENTGVP
LVPVEPDKVEEATEGEN YMLDLQPETTDLYCYEQ
PVESMETTMRSPVFTDN ISEYRHYCYSLYGTTLE
AAVDAGMAMAGQSPVLR QPKKVKRRLFETRELTD
LGEFYNQMMVKAGLNDD GYGGRASDYKSAHKGLK
KTKDIVNGLRSVQTFAD LVGFLLLKYRAREPVTK
SVDPKNYPKKKMEKRFV SSSSTPLLYPSLALPAP
FLYGALLLAEGFYTTGA
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NetChop20S-3.0In vitro digest data from the
constitutive proteasome
Toes et al., J.exp.med. 2001
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Prediction performance
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Predicting proteasomal cleavage
NetChop20S-3.0
NetChop-3.0

• Relative poor predictive performance
• For MHC prediction CC0.92 and AUC0.95

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Proteasome specificity

• NetChop is one of the best available cleavage
  method
• www.cbs.dtu.dk/services/NetChop-3.0

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Cellular Immunity
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What does TAP do?
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TAP affinity prediction

• Transporter Associated with antigen Processing
• Binds peptides 9-18 long
• Binding determined mostly by N1-3 and C terminal
  amino acids

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TAP binding motif matrix
A low matrix entry corresponds to an amino acid
well suited for TAP binding
Peters et el., 2003. JI, 171 1741.
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TAP affinity prediction
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Predicting TAP affinity
9 meric peptides
gt9 meric
ILRGTSFVYV -0.11 0.09 - 0.42 - 0.3 -0.74
Peters et el., 2003. JI, 171 1741.
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Integrating all three steps (protesaomal
cleavage, TAP transport and MHC binding) should
lead to improved identification of peptides
capable of eliciting CTL responses
Integration?
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Identifying CTL epitopes
HLA affinity
Proteasomal cleavage
TAP affinity
1 EBN3_EBV YQAYSSWMY 2.56 1.00 0.03 0.34 0.99
0.02 0.01 0.75 0.94 0.92 2.97 0 2.80 2 EBN3_EBV
QSDETATSH 2.22 0.01 0.28 0.88 0.04 0.83 0.51 0.30
0.11 0.99 -0.80 0 2.28 3 EBN3_EBV PVSPAVNQY 1.55
0.01 0.97 0.01 0.22 0.21 1.00 0.02 0.04 1.00
2.63 0 1.78 4 EBN3_EBV AYSSWMYSY 1.31 0.34 0.99
0.02 0.01 0.75 0.94 0.92 0.09 1.00 3.28 1 1.58 5
EBN3_EBV LAAGWPMGY 1.02 1.00 0.97 0.22 0.01 0.18
0.01 0.06 0.01 1.00 3.01 0 1.27 6 EBN3_EBV
IVQSCNPRY 0.99 0.10 0.97 0.50 0.05 0.01 0.01 0.01
0.02 0.93 3.19 0 1.24 7 EBN3_EBV FLQRTDLSY 0.94
0.46 0.99 0.02 0.82 0.07 0.01 0.63 0.01 0.96
2.79 0 1.18 8 EBN3_EBV YTDHQTTPT 1.15 1.00 0.01
0.42 0.02 0.04 0.01 0.02 0.54 0.14 -0.87 0 1.12 9
EBN3_EBV GTDVVQHQL 0.96 0.01 0.02 0.03 0.99 1.00
0.02 0.46 0.30 1.00 0.53 0 1.09 ...
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(No Transcript)
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Large scale method validation
HIV A3 epitope predictions
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Pathogen and population coverage

• How to hit them all in a few strokes

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HCV Genotypes
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Genotype Variation
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Genotype variation
HIV-1 CRF02_AG (a), HCV genotype 4 (b) and HCV
genotype 1 (c)
de Oliveira et al., Nature 444, 836-837(14
December 2006)
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GenoCover
Select peptide with maximal coverage
Top Scoring Peptides
Genotype 1
Genotype 2
Select peptide with maximal coverage preferring
uncovered strains
Genotype 3
Genotype 4
Genotype 5
Genotype 6
Select peptide with maximal coverage preferring
lowest covered strains
Repeat until the desired number of peptides is
selected
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HCV Results - B7
Genome Coverage
Peptides
Predicted affinity (nM)
Peptide
Genotype 1
QPRGRRQPI
5
4
5
Genotype 2
SPRGSRPSW
43
3
4
Genotype 3
2
3
66
DPRRRSRNL
Genotype 4
3
RARAVRAKL
6
3
Genotype 5
3
TPAETTVRL
38
3
Genotype 6
3
Verified B7 supertype restricted CD8 epitope
in the Los Alamos HCV epitope database
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Population Diversity
http//static.howstuffworks.com/gif/population-six
-billion-1.jpg
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MHC-Cover
Select peptide with maximal MHC coverage
Top Scoring Peptides
HLA-A0101
HLA-A0201
Select peptide with maximal MHC coverage
preferring uncovered MHCs
HLA-A0301
HLA-B0702
HLA-B2705
HLA-B4402
Select peptide with maximal MHC coverage
preferring lowest covered HLAs
Repeat until the desired number of peptides is
selected
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Population diversity
http//www.piperreport.com/archives/Images/Marketi
ng20to20Diverse20Medicare20Population.jpg
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MHC-Cover
Select peptide with maximal population coverage
Top Scoring Peptides
HLA-A0101
HLA-A0201
Select peptide with maximal coverage preferring
uncovered MHCs with highest population coverage
HLA-A0301
HLA-B0702
HLA-B2705
HLA-B4402
Select peptide with maximal coverage preferring
lowest covered HLAs with highest population
coverage
Repeat until the desired number of peptides is
selected
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Epi-select
Select peptide with maximal population coverage
and maximal genotype coverage
Genotype 1
HLA-A0101
Genotype 2
HLA-A0201
Genotype 3
Select peptide with maximal coverage preferring
uncovered MHCs with highest population coverage
and maximal genotype coverage
HLA-A0301
Genotype 4
HLA-B0702
Genotype 5
HLA-B2705
Genotype 6
HLA-B4402
Select peptide with maximal coverage preferring
lowest covered HLAs with highest population
coverage and maximal genotype coverage
Repeat until the desired number of peptides is
selected
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Reaching optimal coverage
HCV Genotypes