Allergenicity Prediction using Sequence Profiles
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1 Max Planck Institute for Molecular Genetics, October 21 st, 2002 Allergenicity Prediction using Sequence Profiles M.B. Stadler University of Bern
2 Overview Allergy What is an allergen/allergic reaction? Generalized profiles Modeling sequence motifs Construction of a profile Allergenicity prediction Current prediction algorithm (FAO/WHO) Profile-based prediction
3 Overview Allergy What is an allergen/allergic reaction? Generalized profiles Modeling sequence motifs Construction of a profile Allergenicity prediction Current prediction algorithm (FAO/WHO) Profile-based prediction
4 Allergens are harmless substances (almost) only proteins inducing IgE immune response rare: ~ proteins (Sp/TrEMBL) ~ 800 sequences < 100 allergens 1 in proteins:
5 Common Allergens house dust mites, pollen & spores, pets, insects, milk, eggs, nuts
6 Immediate Hypersensitivity Reaction Trigger Sensitize B-cell allergen cross-link IgE mediator release mast cell
7 Response to Mediators Bronchi: Constriction Mediators: Histamine Leukotrienes Cytokines Chemokines Enzymes Blood vessels: Vascular leakage (tissue edema)
8 Reaction Rhinitis Asthma Dermatitis Conjunctivitis Anaphylaxis Food Site Nose Lungs Skin Eye Systemic Gut Signs/Symptoms Sneezing, rhinorrhea, nasal itching, congestion Coughing, wheezing, shortness of breath Itching, rash Itching, redness, tearing Hypotension, shock, death Bloating, vomiting, diarrhea, cramping
9 Overview Allergy What is an allergen/allergic reaction? Generalized profiles Modeling sequence motifs Construction of a profile Allergenicity prediction Current prediction algorithm (FAO/WHO) Profile-based prediction
10 Shared Domain Topologies EGF Ig SH2 TcR CD4 IL-1R IgG MHC I FcεRIα β 2 m ICAM-2
11 Sequence-Structure Structure Relationship Domain (Fold): Sequences: Sequence Motif: [FY]-x-C-x-[VA] [VA]-x-H
12 A Generalized Profile position-specific match-, gap- and insert-scores score distribution over sequence space parameters: begin/end: insertion/match: B e E e B i E i I(X) I(*) M(X) M(*) deletion: D state transitions: T B M T B I T B D T B E T M M T M I T M D T M E T I M T I I T I D T I E T D M T D I T D D T D E
13 Manual Construction of Sequence Profiles trusted sequences multiple alignment sequence weights add new sequences PFTOOLS create profile calibrate profile external HMM training new matches? new profile
14 The Birch Allergen Family Clinical cross-reactions include: birch, celery, carrot, apple, hornbeam, hazelnut, alder, apricot, cherry, pear
15 Creating a Bet v 1-Profile1 trusted sequences multiple alignment extensive literature search: 13 allergens: 6 structures 94 sequences
16 Good and Bad Sequence Alignments Sequence based alignment ASTQSPSVFPLTRCCK NIPSNATSVTLGCLAT GYFPEPVMVTWDTGSL NGTTMTLPATTLTLSG HYATISLLTVSGAWAK QMFTCRVAHTPSSTDW VDNKTFSVCSRDFTPP TVKILQSSCDGGGHFP PTIQLLCLVSGYTPGT INITWLEDGQVMDVDL Structure based alignment
17 Creating a Bet v 1-Profile: 1 Structural Alignment trusted sequences multiple alignment 6 structures T_COFFEE structure based alignment guide-profile ASTQSPSVFPLTRCCK NIPSNATSVTLGCLAT GYFPEPVMVTWDTGSL NGTTMTLPATTLTLSG HYATISLLTVSGAWAK 94 sequences QMFTCRVAHTPSSTDW VDNKTFSVCSRDFTPP TVKILQSSCDGGGHFP PTIQLLCLVSGYTPGT INITWLEDGQVMDVDL profile based alignment PFTOOLS
18 Sequence Weights multiple alignment sequence weights create profile Profile should be: focused unbiased outliers similar sequences ++ ++
19 Sequence Weights: Tree Derived R ~ branch length U 0 I 1 +I 2 I 3 +I 4 +I 5 +I 6 +I 7 +I 8 +I 9 +I +I 10 I 3 +I 4 +I 5 I 1 I 2 I 3 I 4 I 5 I 6 I 7 I 8 I 9 I
20 Sequence Weights: Voronoi
21 Empiric Profile Calibration create profile calibrate profile: search randomized sequence database Swiss-Prot, window shuffled fit EVD to scores p( x) = λe λ λ ( ) ( x µ x µ e ) λ ( x µ ) e use EVD-parameters to normalize scores S norm R 1 Snorm = R R x E( x, A) = A 10 A ln λµ = N ln10 R 2 λ = ln10 x: raw score A: no. of residues N: no. of sequences
22 Normalized Score and E-value R1 R2x E( x, A) = A 10 Swiss-Prot 40: A= x=814 S norm =6.5 E-value=10
23 Profile Construction is an Iterative Process trusted sequences multiple alignment sequence weights add new sequences create profile external HMM training calibrate profile new matches? new profile
24 FHA Domain Profile: PS50006 Hofmann & Bucher, 1995, TIBS Database Entry Profile 1 weight score Profile 2 weight score Profile 3 weight score Profile 4 weight score Profile 5 weight score CDS1_SCHPO FHL1_YEAST FKH1_YEAST FKH2_YEAST FRAH_ANASP KAPP_ARATH KI67_HUMAN MNF_MOUSE SPK1_YEAST YHR5_YEAST YKI5_CAEEL HUMKIAA10_1 MLB1770_16 SC9346_10 SCCXIV38K_16 SCD9717_7 SCPPR1GEN_4 SPAC17G8_10 SYCSLRG_6 SYCSLRG_63 YSCL8083_15 YSCL9470_15 B Highest false positive
25 PS50006 continued PS50006 continued score weight score weight score weight score weight score weight Profile 10 Profile 9 Profile 8 Profile 7 Profile 6 Database Entry CDS1_SCHPO FHL1_YEAST FKH1_YEAST FKH2_YEAST Highest false positive B YSCL9470_ YSCL8083_ SYCSLRG_ SYCSLRG_ SPAC17G8_ SCPPR1GEN_ SCD9717_ SCCXIV38K_ SC9346_ MLB1770_ HUMKIAA10_ YKI5_CAEEL YHR5_YEAST SPK1_YEAST MNF_MOUSE KI67_HUMAN KAPP_ARATH FRAH_ANASP
26 Overview Allergy What is an allergen/allergic reaction? Generalized profiles Modeling sequence motifs Construction of a profile Allergenicity prediction Current prediction algorithm (FAO/WHO) Profile-based prediction
27 Allergens in Transgenic Food Brazil nut Soy Nordlee et al., 1996, N Engl J Med tg-soy Methionine-rich 2S Albumin Met-rich allergic reaction in nut-sensitized patients
28 Prediction of Allergens No common: Structure Biochemical properties no direct prediction indirect prediction: similarity with known allergen potential cross-reactivity potentially allergenic
29 Immunological Cross-reactivity reactivity cross-reactive antibody antigen A birch pollen allergen (Bet v 1, PDB:1BTV) antigen B cherry allergen (Pru av 1, PDB:1E09)
30 Prediction of Cross-reactivity reactivity linear sequence single loops secondary structure elements M PEPV TQSPSVFPLTRCC V TYFPEPVM HY KNIPSNATSVTLGCLATGYF LTLSG T AT P V W DTGSL surface shape physico-chemical properties
31 Cross-reactivity reactivity and Sequence Similarity Sequence-based Clustering Bet v 1 - cluster Clustering ALL1_APIGR Api g 1 ALL2_APIGR Api g 2 celery BV1A_BETVE BV1B_BETVE BV1C_BETVE BV1D_BETVE BV1E_BETVE BV1F_BETVE Bet v 1 birch BV1G_BETVE BV1J_BETVE BV1K_BETVE BV1L_BETVE BV1M_BETVE DAU1_DAUCA Dau c 1 carrot MAL1_MALDO Mal d 1 apple MPA1_CARBE Car b 1 hornbeam MPA2_CARBE Car b 1 MPAA_CORAV Cor a 1 hazelnut MPAG_ALNGL Aln g 1 alder PRU1_PRUAR Pru ar 1 apricot PRU1_PRUAV Pru av 1 cherry PYR1_PYRCO Pyr c 1 pear
32 Proposed Allergenicity Evaluation (WHO/FAO) ASTQSPSVFPNIPSNATSVTLGCLAT GYFPEPVMVTTRCCKNIPSNATSVTL GCLATGYFPEPVMVTNIPSNATSVTL protein of GCLATGYFPEPVMVTWDTGSLNGTTM TLPATTLTLSGHYATISLLTVSGAWA KQMFTCRVAHTPSSTDWVDNKTFSVC interest SRDFTPPTVKILQSSCDGGGHFPPTI? Allergens identity-test: test: n = 6 contiguous amino acids similarity-test: test: 35 % (80 residues)
33 Allergen Prediction According to Guidelines Database: Adb Swiss-Prot Rice trgen (human) Description: allergen general protein rice genome human genome database database (TIGR OsGI) (translated) #Proteins: allergens 98.6 % 67.3 % 75.9 % 42.9 % (predicted) clinical observation: < 0.5 %
34 Performance of Current Allergen Prediction performance 100% recall: % true allergens 80% predicted to be an allergen 60% precision: % true allergens of 40% predicted allergens identity length n unsuitable for allergenicity prediction.
35 Allergen Database (Adb) download HTML lists extract accessions download sequences remove redundancy build local database Adb Data source (February 11 th, 2002) (isoallergens) (Swiss-Prot allergens) (food allergens) (non-food allergens) add_list.txt Total accessions: Database Swiss-Prot Swiss-Prot (variants) GenBank PIR skipped: redundant unreachable annotation problems Total retrieved sequences: #accessions #sequences
36 Automatic Identification of Allergen Profiles Adb Dataset motif discovery (MEME) remaining sequences motif collect remove matches Matches search dataset Motives
37 52 Allergen Profiles Profile Identifier MEME E-value Matching allergens Predominant PROSITE matches AM Pathogenesis-related Bet v 1 family AM Profilins Pollen proteins (Ole e I) AM Globins AM none AM SCP/Tpx-1/Ag5/PR-1/Sc7
38 Profile-based Allergenicity Prediction RDFTPPTVKILQSSCDGGGHFPPTIQLL CLVSGYTPGTINITWLEDGQVMDVDLST query protein ASTTQEGELASTQSELTLSQKHWLSDRT 52 profiles profile match? yes allergens: no 83% 17% 135 sequences pair match? no yes non-allergen allergen
39 Performance of Prediction: Random Sequences Profile-based FAO/WHO 100% performance 80% 60% 40% BLAST E-value cut-off recall precision identity length n
40 Performance of Prediction: Swiss-Prot Sequences Prediction method FAO/WHO Profile- based Predicted Allergens % % True Allergens % %
41 Conclusion Allergen Database (Adb): - most complete allergen sequence resource - semi-automated WHO/FAO method for allergenicity evaluation: - unspecific (precision = 0.5%) - algorithmic limitation Profile-based prediction: - improved performance (precision = 8.6%)
42 Outlook Improved prediction: - pure profile based approach - two phase prediction (fold, surface) Search for unknown allergens: - xeno- vs. autologous structures - production of pan-allergic allergic structures (for diagnosis and therapy)
43 institute of immunology bern Prof. Dr. B.M. Stadler Dr. S. Miescher Dr. M. Vogel Michaela Fux Lorenz Scheppler Tomasz Bobrzynski Elsbeth Gautschi Andreas Hofmann Pamela Marti Jacqueline de Sa Diana Arnold Evelyne Aufdenblatten Dr. Philipp Bucher SIB, Lausanne
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