Prediction of B cell epitopes

Pernille Haste Andersen

Immunological Bioinformatics

CBS, DTU

pan@cbs.dtu.dk

B cells and antibodies

Antibodies are produced by B lymphocytes (B cells)

Antibodies circulate in the blood

They are referred to as “the first line of defense” against infection

Antibodies play a central role in immunity by attaching to pathogens and recruiting effector systems that kill the invader

What is a B cell epitope?

Antibody Fabfragment

B cell epitope

B cell epitopes

Accessible and recognizable structural feature of a pathogen molecule (antigen)

Antibodies are developed to bind the epitope with high affinity by using the complementarity determining regions (CDRs)

Motivations for prediction of B cell epitopes

Prediction of B cell epitopes can potentially guide experimental epitope mapping

Predictions of antigenicity in proteins can be used for selecting subunits in rational vaccine design

Predictions of B cell epitopes may also be valuable for interpretation of results from experiments based on antibody affinity binding such as ELISA, RIA and western blotting

Computational Rational Vaccine Design

>PATHOGEN PROTEINKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNF

Rational Vaccine Design

B cell epitopes, linear or discontinuous?

Classified into linear (~10%) and discontinuous epitopes (~90%)

Databases: AntiJen, IEDB, BciPep, Los Alamos HIV database, Protein Data Bank

Large amount of data available for linear epitopes

Few data available for discontinuous epitopes

In general, B cell epitope prediction methods have relatively low performances

Discontinuous B cell epitopes

SLDEKNSVSVDLPGEMKVLVSKEKNKDGKYDLIATVDKLELKGTSDKNNGSGVLEGVKADKCKVKLTISDDLGQTTLEVFKEDGKTLVSKKVTSKDKSSTEEKFNEKGEVSEKIITRADGTRLEYTGIKSDGSGKAKEVLKG

• ..\Discotope\1OSP_epitope\1OSP_epitope.psw

An example: The epitope of the outer surface protein A from Borrelia Burgdorferi (1OSP)

A data set of 3D discontinuous epitopes

A data set of 75 discontinuous epitopes was compiled from structures of antibodies/protein antigen complexes in the PDB

The data set has been used for developing a method for predictions of discontinuous B cell epitopes

Since about 30 of the PDB entries represented Lysozyme, I have used homology grouping (25 groups of non-homologous antigens) and 5 fold cross-validation for training of the method

Performance was measured using ROC curves on a per antigen basis, and by weighted averaging of AUC values

Epitope log-odds ratios

Frequencies of amino acids in epitopes

compared to frequencies of non-epitopes

Several discrepancies compared to the Parker hydrophilicity scale which is often used for epitope prediction

Both methods are used for predictions using a sequential average of scores

Predictive performance of B cell epitopes:Parker 0.614 AUCEpitope log–odds 0.634 AUC

3D information: Contact numbers

Surface exposure andstructural protrusion canbe measured by residuecontact numbers

The predictive performance:

Parker 0.614 AUCEpitope log–odds 0.634 AUCContact numbers 0.647 AUC

DiscoTope : Prediction of Discontinuous epiTopes using 3D structures

A combination of:– Sequentially averaged epitope log-

odds values of residues in spatial proximity

– Contact numbers

-0.145

+0.346+1.136

+0.691+0.346+1.136+1.180+1.164

Contact number : K 10

DiscoTope prediction value

Sum of log-odds values

.LIST..FVDEKRPGSDIVED……ALILKDENKTTVI.

DiscoTope : Prediction of Discontinuous epiTopes

Improved prediction of residues in discontinuous B

cell epitopes in the data set

The predictive performance on B cell epitopes:

Parker 0.614 AUC

Epitope log–odds 0.634 AUC

Contact numbers 0.647 AUC

DiscoTope 0.711 AUC

Evaluation example AMA1

• Apical membrane antigen 1 from Plasmodium falciparum (not used for training/testing)

• Two epitopes were identified using phage-display, point-mutation (black side chains) and sequence variance analysis (side chains of polyvalent residues in yellow)

• Most residues identified as epitopes were successfully predicted by DiscoTope(green backbone)

DiscoTope is available as web server: http://www.cbs.dtu.dk/services/DiscoTope/

..\Discotope\1Z40_epitope\1Z40_movie.mov

Future improvements

Add epitope predictions for protein-protein complexes

Visualization of epitopes integrated in web server

Testing a score for sequence variability fx based on entropy of positions in the antigens

Combination with glycosylation site predictions

Combination with predictions of trans-membrane regions

Assembling predicted residues into whole epitopes

Presentation of the web server

Presentation of the web server output

Acknowledgements

DiscoTope

Ole Lund Ideas, supervision and support

Morten Nielsen Ideas, development of method and web server

Nicholas Gauthier Improving the method, improving the web server