Epitope discovery Using predicted MHC binding
SARS corona virus
The 2003 outbreak
The disease Lung Pathology Inflammatory exudation in alveoli and interstitial spaces Monocytic and lymphocytic infiltration of lung tissue Hyperplasia of alveolar epithelial cells and fibrous tissue Fibrosis of lung tissue http://www.brown.edu/courses/bio_160/projects2004/sars/sars-cov/pathology.htm
SARS corona virus Cell Research (2003); 13(3):141-145
SARS genome 0 5 10 15 20 25 30 gene 1a gene 1b S mrnas3-9 SARS-CoV mrna1 pp1a, pp1ba mrna2 S protein mrna3 mrna4 E protein mrna5 M protein mrna6 mrna7 mrna8 mrna9 N protein SARS-CoV genome organization. The structure of the SARS viral RNA is organized into 13 15 open reading frames (ORFs) and contains an overall amount of approximately 30,000 nucleotides. The sequence can be separated into different elements and genomic and subgenomic mrnas. Groneberg et al. Respiratory Research 2005 6:8 doi:10.1186/1465-9921-6-8
Status of CBS prediction methods 2003 A*0101 PSSM A*0201 ANN A*0301 PSSM A*2402 PSSM B*0702 PSSM B*1501 PSSM B*4001 PSSM B*5801 P B*2705 No-predictions
Selection scheme Full genome 9mers predicted Top 15 sorted by affinity with C-term NetChop score >0.5
Timeframe Genome 15. April 2003 Predictions ready April 27 Measurements ready june 15.
Results ANNs
Validation of binders as SARS died out epitopes Few infected kept proprietary
SARS natural host?
Can we use MHC binding alone in epitope discovery? NATURE BIOTECHNOLOGY VOLUME 24 NUMBER 7 JULY 2006 NATURE BIOTECHNOLOGY VOLUME 24 NUMBER 7 JULY 2006
Pox - a test example
Smallpox Incubation period before symptoms:10-14 days Symptoms high fever, headache, backache, and vomiting, rash (pox) on the face and arms that spreads to the trunk How it would be spread Aerosol or person-to-person, potentially by a terrorist- martyr. It is highly contagious. However, smallpox victims show clear signs of the disease, and anyone who came in contact with them could be vaccinated post-exposure. Treatment: There is no current treatment against the smallpox virus. Vaccination given 3-5 days post-exposure can prevent the disease. Vaccine:Vaccine exists but is currently not recommended for the general public. Stockpiles of vaccine are being increased. No one in the U.S. has been vaccinated since 1972, and people vaccinated before then have likely lost immunity.
Mouse disease model www.crude.co.nz/ images/mouse%20copy.gif
Pox genome and proteome http://www.scq.ubc.ca/wp-content/uploads/2006/08/smallpoxvirus.gif
Experimental design Matrix prediction method Rank all possible 8-, 9- and 10-mers from the VACV- WR sequence according to their predicted abilities to bind H-2 Kb (8- and 9-mers) and Db (9-and 10-mers) The median rank in the four predictions was used to select the top 1% of peptides within each size-based class, comprising 2,256 peptides Split into pools that were each tested for antigenicity by interferon (IFN)-γ-ELISPOT assays
CTL response - Pox
45 % of the response is generated by 5 peptides
95 % of response generated by 49 peptides
Convoluted to single peptide map
Overview
Binding affinity is a good filtering method Makes an almost comprehensive epitope mapping possible for a larger organism 95 % might be overestimated due to the pooling effect
Prediction - Validation scheme is a fast and efficient way to identify CTL epitopes from emerging pathogens What we need is a general way to use selected epitopes in vaccines