Finding Data in the IEDB 3.0. Kerrie Vaughan, PhD - Sr. Biocurator/Meta-Analysis Nima Salimi, MS - Sr. Biocurator/Curation Mgr

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1 Finding Data in the IEDB 3.0 Kerrie Vaughan, PhD - Sr. Biocurator/Meta-Analysis Nima Salimi, MS - Sr. Biocurator/Curation Mgr 1

2 Finding Data in the IEDB 3.0 IEDB Overview Content and Organization IEDB Search Interface Introduction to the Analysis Resource 2

3 Overview for the Day Part I IEDB 3.0 Home page search Exploring the query results Finders Specialized search Additional features Part II Immunome Browser Example queries (static) Part III Exercises (live) Participant-derived queries (live) 3

4 Part I Detailed overview of IEDB search interfaces 4

5 To better understand your interests/needs Familiarity with the site? First time users? How many use it for queries? Tools? Both? Downloads of database? License interest? 5

6 The 3.0 Home Page Bjoern and Randi Kerrie and Nima Day 2 6

7 Home Page Search Interface Search by: Epitope sequence Antigen Host MHC restriction Disease Assay type 7

8 Search from Results Page Search panes are also present along the left margin within the Results Page 1. Enables refinement of initial query 2. Allows for more complex search (e.g. specific assay) 3. Allows for Specialized Searches (e.g. mab by name) 8

9 Default is Any Epitope Sequence Search Type in sequence Use radio button to specify Linear Discontinuous Non-peptidic (carbs/lipids) Search for exact or homologous results 9

10 Antigen Search Pathogen (virus, bacteria) Mammals (self-ag) Allergen source (grass) Protein of interest (source of epitope) Click field, type in name, auto-complete 10

11 Assay Search Select response type of interest at high level (T, B or MHC ligand) Default is All and Positive only Type assay of interest into the text box Click Finder to access finder if you cannot immediately find the one you want 11

12 MHC Restriction Search Search all reported restrictions Specify class Use text box to find allele with auto-complete Use Finder to explore specific alleles 12

13 Host Search Search for host of interest Human data Animal models Default will return Any Specific species/strains (ex. Tg mice) are searchable using text box or Finder Home page provides basics 13

14 Search by Disease Represents clinical status of a host: Patient history Known animal model Unique feature Allergy Autoimmunity Can assess differential reactivity Animal model v. human Disease Tree developed by IEDB 14

15 Exploring the Results Page Query interface on left to refine search or access Finder Filters track query parameters along the top Tabs for Epitope, Antigen, Assay and Reference provide quick summary of content in () Export of data per tab is available in Excel format 15

16 Using Finders and Data Trees Finders are a unique feature of the IEDB that provide standardization and hierarchical organization for data captured therein Allows users to search an enormous amount of data at any level of granularity by making use of collapsible data trees Data tree ontological/taxonomical-based data organizer with parent/child node relationships Used to organize: Antigens (protein accessions, SwissProt, PDB) Non-proteins (ChEBI) Organisms (NCBI taxonomy) Alleles Assays Disease (Disease Ontology, DO ids) They work behinds the scenes and are also accessible to the user, as well 16

17 Accessing Finders Mouse over pane to expand Click search on Home Page to access Finders On the Results Page 17

18 Non-Peptidic Epitope Finder Click Tree View to open finder (below) Search for non-protein chemical entities shown to react with B and T cells: e.g. metal allergens, drugs/compounds, glycolipids, etc. Chemical Data Tree Type name Click to Find 18

19 Organism Finder Click Tree View to open finder (below) Used to search for: epitope source immunogen if organism assay antigen source Links to NCBI taxonomy Open tree to search by taxonomic group bacteria, viruses or eukaryotes Type organism name Click to Find 19

20 Organism Finder Click highlight in tree to see breakdown of available genotypes Can click Plus sign and then Apply to add criteria 20

21 Organism Data Tree Click to open successive nodes to find specific strain or use high node to look at all available 21

22 Molecule Finder Click Tree View to open finder (below) Used to search for: epitope source immunogen if protein assay antigen source Links to Uniprot/Swissprot Type protein Type organism 22

23 Molecule Finder Use top row to sort Click Highlight in Tree to see what s available 23

24 Example of Antigen Tree Click high node Hemagglutinin to retrieve all HA from all flu 24

25 Assay Finder Used to find specific assay type within the broader category of B cell, T cell or MHC ligand Examples: neutralization, cytolysis, binding versus MS/HPLC elution Categories based on the type of activity defined in the assay 25

26 Allele Finder Used to specify: MHC restriction defined in assay Alleles from 15 species to date Can search at level of: Species Class (I, II, non-classical) Serotype/allele 26

27 Host Finder Subject or animal from whom the immune response was defined Humans and animal models (ex. Tg mice) examples 27

28 Disease Finder Broad disease categories Specific disease types (RA, asthma) Includes animal models (EAE) Easy way to find data for non-infectious disease example 28

29 Reference Search Search by paper of interest 29

30 Specialized Searches 1. Details searches Search all database fields Formulate more specific queries (e.g. antibody isotypes/names, effector cell phenotypes) 2. Identifier search Query using unique IDs

31 Specialized Search Epitope Details Epitope fields Reference fields 31

32 Search by epitope name, start/stop positions, etc. Search for analogs or mimotopes 32

33 Search by author(s), journal, etc. 33

34 Specialized Search Assay Details (T, B, MHC) How did host acquire immune reactivity? Immunized, naturally infected, etc. Specify the immunogen (epitope, protein, organism, etc.) Search by specific host disease Search by specific assay type Specify effector cells, mab name, or antibody isotype(s) Specify the assay antigen (epitope, protein, organism, etc.) 34

35 Identifier Search A quick way to retrieve data by using an inventory number Unique identifiers created by IEDB Unique identifiers from other resources 35

36 Identifier Search

37 Break 11:00-11:15am 37

38 Immunome Browser (IB) The IB is a unique analysis tool that is integrated into query interface What is it? Immunome - totality of immune reactivities on an organismal level What is it for? What are potentially immunodominant epitopes? No straightforward answer, really Our Approach use host response frequency data to a give indication of overall epitope prominence How does it work? Plots the response frequency score (RFscore) for epitopes from a particular query along the length of antigen using a reference proteome Designed to provide way to identify and visualize an optimized subset of data using specific user-defined selection criteria 38

39 Immunome Browser Example Hepatitis C virus (HCV) Genomic polyprotein ~3,000 amino acids 4,212 epitopes captured in the IEDB This abundance of data reflects iterative coverage by multiple labs, assays, hosts, etc. How can you see the choice trees for the forest? Query input selection criteria can be broad or very stringent 39

40 Immunome Browser How it works A HCV search from the Home Page yields 4,212 epitopes derived from Genome polyprotein Represents 12,000 assays from 548 papers Click Immunome Browser icon to map these epitopes to system-provided reference proteome 40

41 Y-axis = RFscore X-axis = epitope residue position Data represents all epitope, all assays, all hosts Below shows coverage by assay Refine query to eliminate (specify host) or differentiate (B cell versus T cell) 41

42 Scroll down to see table of RF scores 42

43 Part II Example Queries 43

44 Example 1- Search for the epitope ASNENMETM Elements highlighted: Sequence search Homology search Results table Summary Filter and drill down Data details 44

45 Results Page - summarized on tabs 5 structures (modifications) Source protein = NP 362 assays 132 references Can then click through the tabs to review data 45

46 Assay Tab 312 T cell assays 50 MHC Ligand assays Use columns to review high level Click on assay ID to see all details 46

47 References tab Listed by most recent Link to PubMed (blue) Use columns to review high level Click on Ref ID to see all details 47

48 New filtering feature Click on funnel to lock onto epitope of interest Tabs will re-set data for only that epitope 48

49 Alternatively, you can modify the search to look for homologous peptides 49

50 Refined query at 70% homology reveals numerous analogs of the flu epitope Identify analog of interest Filter on this epitope 50

51 A total of 4 assays reported for this analog 2 T cell (CTL) and MHC ligand Explore T cell first. Click on the assay ID to drill down into the context of interest Click other assay tabs to review all relevant assay types 51

52 Full details for this assay: Reference Epitope Host Immunization Assay type Antigen 52

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54 Example 2 What T cell epitopes have been associated with treatment of allergy? 2. Scroll down to Disease pane. Select high node allergic disease 1. Start on Results Page to access Assay Finder. Select T Cell and type in treatment 54

55 Search Results 111 epitopes associated with treatment of allergy in all hosts. Click Antigen tab to see summary. 55

56 Click on the Antigen tab to get a summary of all allergens Pollens, dust mite, bee sting, grass, fungus Can click on funnel to explore epitope OR allergen of interest Another option map results using Immunome Browser 56

57 Click on the Assay tab to sort by host 57

58 Example T Cell Details Search Find Rift Valley fever virus T cell epitopes tested specifically on CD8 + T cells and defined in humans.

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64 Example T Cell Details Search Find Rift Valley fever virus T cell epitopes tested specifically on CD8 + T cells and defined in humans. Have tetramers been made with any of these epitopes and been shown to work?

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67 Example B Cell Details Search Find Influenza A virus epitopes recognized by neutralizing human monoclonal antibodies.

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77 Lunch 12:35-1:30pm 77

78 Part III Follow-along exercises Participant queries 78

79 Infectious disease What antibody P. falciparum epitopes have been defined for humans? What protective T cell epitopes have been defined against TB in mice? From what antigens? What mabs have been described for Dengue virus? What tetramers have been used in the context of influenza A virus? What alleles? 79

80 Autoimmunity What human data are available for multiple sclerosis? What antigens have been mapped for T cell epitopes? Have therapeutic epitopes been identified? Are there immunodominant regions defined for insulin in humans with T1D? 80

81 Allergy What antibody epitopes have been defined in the context of almond allergy? Can these be mapped to the 3D structure? 81

82 Cancer-related data Programmatically, cancer is not within the scope of the IEDB. The IEDB does contain relevant data as part of in-scope papers (cancer from ID, melanocyte Ags) How would I find cancer epitopes? Search by antigen e.g. Pmel Search by disease ovarian cancer 82

83 Queries with vaccine development in mind In vitro correlates of protection Neutralization, CTL, IFNg, etc. In vivo challenge assays Survival, decreased pathogen burden Treatment Assays (prophylactic/therapeutic) Coverage Population (informatic) Immunome Browser 83

84 Exercise 1 - Nima Given a protein of interest, determine which T cell and B cell epitopes have been identified. Protein of interest: pm45 [Murid herpesvirus 1] GI: MDRQPKVYSDPDNGFFFLDVPMPDDGQGGQQTATTAAGGAFGVGGGHSVPYVRIMNGVSGIQIGNHNAMSIAS CWSPSYTDRRRRSYPKTATNAAADRVAAAVSAANAAVNAAAAAAAAGGGGGANLLAAAVTCANQRGCCGGNG GHSLPPTRMPKTNATAAAAPAVAGASNAKSDNNHANATSGAGSAAATPAATTPAATAVENRRPSPSPSTASTAPC DEGSSPRHHRPSHVSVGTQATPSTPIPIPAPRCSTGQQQQQPQAKKLKPAKADPLLYAATMPPPASVTTAAAAAVA PESESSPAASAPPAAAAMATGGDDEDQSSFSFVSDDVLGEFEDLRIAGLPVRDEMRPPTPTMTVIPVSRPFRAGR DSGRDALFDDAVESVRCYCHGILGNSRFCALVNEKCSEPAKERMARIRRYAADVTRCGPLALYTAIVSSANRLIQT DPSCDLDLAECYVETASKRNAVPLSAFYRDCDRLRDAVAAFFKTYGMVVDAMAQRITERVGPALGRGLYSTVVM MDRCGNSFQGREETPISVFARVAAALAVECEVDGGVSYKILSSKPVDAAQAFDAFLSALCSFAIIPSPRVLAYAGFG GSNPIFDAVSYRAQFYSAESTINGTLHDICDMVTNGLSVSVSAADLGGDIVASLHILGQQCKALRPYARFKTVLRIY FDIWSVDALKIFSFILDVGREYEGLMAFAVNTPRIFWDRYLDSSGDKMWLMFARREAAALCGLDLKSFRNVYEKM ERDGRSAITVSPWWAVCQLDACVARGNTAVVFPHNVKSMIPENIGRPAVCGPGVSVVSGGFVGCTPIHELCINLE NCVLEGAAVESSVDVVLGLGCRFSFKALESLVRDAVVLGNLLIDMTVRTNAYGAGKLLTLYRDLHIGVVGFHAVMN RLGQKFADMESYDLNQRIAEFIYYTAVRASVDLCMAGADPFPKFPKSLYAAGRFYPDLFDDDERGPRRMTKEFLE KLREDVVKHGIRNASFITGCSADEAANLAGTTPGFWPRRDNVFLEQTPLMMTPTKDQMLDECVRSVKIEPHRLH EEDLSCLGENRPVELPVLNSRLRQISKESATVAVRRGRSAPFYDDSDDEDEVACSETGWTVSTDAVIKMCVDRQP FVDHAQSLPVAIGFGGSSVELARHLRRGNALGLSVGVYKCSMPPSVNYR

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87 Exercise 2 - Nima Demo searching binding vs. elution data using assay tree.

88 Participant queries Live demos of queries submitted by the group from database standpoint (versus Tools) 88

89 Finding Data in the IEDB 3.0 IEDB Overview Content and Organization IEDB Search Interface Introduction to the Analysis Resource 89