Epitope discovery. Using predicted MHC binding CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

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1 Epitope discovery Using predicted MHC binding

2 SARS corona virus

3 The 2003 outbreak

4 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

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7 SARS corona virus Cell Research (2003); 13(3):

8 SARS genome 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 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 :8 doi: /

9 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

10 Selection scheme Full genome 9mers predicted Top 15 sorted by affinity with C-term NetChop score >0.5

11 Timeframe Genome 15. April 2003 Predictions ready April 27 Measurements ready june 15.

12 Results ANNs

13 Validation of binders as SARS died out epitopes Few infected kept proprietary

14 SARS natural host?

15 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

16 Pox - a test example

17 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.

18 Mouse disease model images/mouse%20copy.gif

19 Pox genome and proteome

20 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

21 CTL response - Pox

22 45 % of the response is generated by 5 peptides

23 95 % of response generated by 49 peptides

24 Convoluted to single peptide map

25 Overview

26 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

27 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