Databases for T-Cell Epitopes

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1184)

Abstract

Modem immunology and vaccinology incorporate immunoinformatics techniques to give insights into immune systems and accelerate vaccine design. Databases managing epitope data in a structured form with immune-related annotations including sequences, alleles, source organisms, structures, and diseases could be the most crucial part of immunoinformatics offering data sources for the analysis of immune systems and development of prediction methods. This chapter provides an overview of publicly available databases of T-cell epitopes including general databases, pathogen- and tumor-specific databases, and 3D structure databases.

Key words

Database Immunogenicity Immunoinformatics Major histocompatibility complex Pathogen T-cell epitope Transporter associated with antigen processing Tumor Vaccine 

References

  1. 1.
    Sette A, Peters B (2007) Immune epitope mapping in the post-genomic era: lessons for vaccine development. Curr Opin Immunol 19(1):106–110PubMedCrossRefGoogle Scholar
  2. 2.
    Salit RB, Kast WM, Velders MP (2002) Ins and outs of clinical trials with peptide-based vaccines. Front Biosci 7:e204–e213PubMedCrossRefGoogle Scholar
  3. 3.
    Wonderlich J, Shearer G, Livingstone A, Brooks A (2006) Induction and measurement of cytotoxic T lymphocyte activity. Curr Protoc Immunol. Chapter 3:Unit 3.11Google Scholar
  4. 4.
    Brunner KT, Mauel J, Cerottini JC, Chapuis B (1968) Quantitative assay of the lytic action of immune lymphoid cells on 51-Cr-labelled allogeneic target cells in vitro; inhibition by isoantibody and by drugs. Immunology 14(2): 181–196PubMedCentralPubMedGoogle Scholar
  5. 5.
    Matzinger P (1991) The JAM test. A simple assay for DNA fragmentation and cell death. J Immunol Methods 145(1–2):185–192PubMedCrossRefGoogle Scholar
  6. 6.
    Kruisbeek AM, Shevach E, Thornton AM (2004) Proliferative assays for T cell function. Curr Protoc Immunol. Chapter 3:Unit 3.12Google Scholar
  7. 7.
    Anthony DD, Milkovich KA, Zhang W, Rodriguez B, Yonkers NL, Tary-Lehmann M, Lehmann PV (2012) Dissecting the T cell response: proliferation assays vs cytokine signatures by ELISPOT. Cells 1(2):127–140PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Czerkinsky CC, Nilsson LA, Nygren H, Ouchterlony O, Tarkowski A (1983) A solid-phase enzyme-linked immunospot (ELISPOT) assay for enumeration of specific antibody-secreting cells. J Immunol Methods 65(1–2): 109–121PubMedCrossRefGoogle Scholar
  9. 9.
    Kalyuzhny AE (2005) Handbook of ELISPOT: methods and protocols. Humana, Totowa, NJCrossRefGoogle Scholar
  10. 10.
    Li Pira G, Ivaldi F, Moretti P, Manca F (2010) High throughput T epitope mapping and vaccine development. J Biomed Biotechnol 2010: 325720PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Rodda SJ (2002) Peptide libraries for T cell epitope screening and characterization. J Immunol Methods 267(1):71–77PubMedCrossRefGoogle Scholar
  12. 12.
    Kiecker F, Streitz M, Ay B, Cherepnev G, Volk HD, Volkmer-Engert R, Kern F (2004) Analysis of antigen-specific T-cell responses with synthetic peptides—what kind of peptide for which purpose? Hum Immunol 65(5): 523–536PubMedCrossRefGoogle Scholar
  13. 13.
    Lundegaard C, Lund O, Nielsen M (2012) Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy? Expert Rev Vaccines 11(1):43–54PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Tung CW, Ziehm M, Kamper A, Kohlbacher O, Ho SY (2011) POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinformatics 12:446PubMedCentralPubMedCrossRefGoogle Scholar
  15. 15.
    Tung CW, Ho SY (2007) POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties. Bioinformatics 23(8):942–949PubMedCrossRefGoogle Scholar
  16. 16.
    Schonbach C, Koh JL, Flower DR, Wong L, Brusic V (2002) FIMM, a database of functional molecular immunology: update 2002. Nucleic Acids Res 30(1):226–229PubMedCentralPubMedCrossRefGoogle Scholar
  17. 17.
    Brusic V, Rudy G, Harrison LC (1998) MHCPEP, a database of MHC-binding peptides: update 1997. Nucleic Acids Res 26(1): 368–371PubMedCentralPubMedCrossRefGoogle Scholar
  18. 18.
    Lata S, Bhasin M, Raghava GP (2009) MHCBN 4.0: a database of MHC/TAP binding peptides and T-cell epitopes. BMC Res Notes 2:61PubMedCentralPubMedCrossRefGoogle Scholar
  19. 19.
    Reche PA, Zhang H, Glutting JP, Reinherz EL (2005) EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology. Bioinformatics 21(9):2140–2141PubMedCrossRefGoogle Scholar
  20. 20.
    Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50(3–4):213–219PubMedCrossRefGoogle Scholar
  21. 21.
    Schuler MM, Nastke MD, Stevanovikc S (2007) SYFPEITHI: database for searching and T-cell epitope prediction. Methods Mol Biol 409:75–93PubMedCrossRefGoogle Scholar
  22. 22.
    Blythe MJ, Doytchinova IA, Flower DR (2002) JenPep: a database of quantitative functional peptide data for immunology. Bioinformatics 18(3):434–439PubMedCrossRefGoogle Scholar
  23. 23.
    McSparron H, Blythe MJ, Zygouri C, Doytchinova IA, Flower DR (2003) JenPep: a novel computational information resource for immunobiology and vaccinology. J Chem Inf Comput Sci 43(4):1276–1287PubMedCrossRefGoogle Scholar
  24. 24.
    Toseland CP, Clayton DJ, McSparron H, Hemsley SL, Blythe MJ, Paine K, Doytchinova IA, Guan P, Hattotuwagama CK, Flower DR (2005) AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res 1(1):4PubMedCentralPubMedCrossRefGoogle Scholar
  25. 25.
    Korber B, Moore J, Brander C, Koup R, Haynes B, Walker BD (1998) HIV Molecular Immunology Database. Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico. LA-UR 99-586Google Scholar
  26. 26.
    Bhasin M, Lata S, Raghava GP (2007) Searching and mapping of T-cell epitopes, MHC binders, and TAP binders. Methods Mol Biol 409:95–112PubMedCrossRefGoogle Scholar
  27. 27.
    Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B (2010) The immune epitope database 2.0. Nucleic Acids Res 38(Database issue): D854–D862PubMedCentralPubMedCrossRefGoogle Scholar
  28. 28.
    Ponomarenko J, Papangelopoulos N, Zajonc DM, Peters B, Sette A, Bourne PE (2011) IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res 39(Database issue):D1164–D1170PubMedCentralPubMedCrossRefGoogle Scholar
  29. 29.
    Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B (2012) Immune epitope database analysis resource. Nucleic Acids Res 40(Web Server issue):W525–W530PubMedCentralPubMedCrossRefGoogle Scholar
  30. 30.
    Ansari HR, Flower DR, Raghava GP (2010) AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res 38(Database issue):D847–D853PubMedCentralPubMedCrossRefGoogle Scholar
  31. 31.
    Yang B, Sayers S, Xiang Z, He Y (2011) Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Res 39(Database issue):D1073–D1078PubMedCentralPubMedCrossRefGoogle Scholar
  32. 32.
    Hraber PT, Leach RW, Reilly LP, Thurmond J, Yusim K, Kuiken C, Los Alamos HIV database team (2007) Los Alamos hepatitis C virus sequence and human immunology databases: an expanding resource for antiviral research. Antivir Chem Chemother 18(3):113–123PubMedGoogle Scholar
  33. 33.
    van der Bruggen P, Stroobant V, Vigneron N, Van den Eynde B (2013) Peptide database: T cell-defined tumor antigens. Cancer Immun 13:15PubMedCentralPubMedGoogle Scholar
  34. 34.
    Bioinformatics Core at Cancer Vaccine Center D-FCI (2009) TANTIGEN: Tumor T cell Antigen DatabaseGoogle Scholar
  35. 35.
    Govindarajan KR, Kangueane P, Tan TW, Ranganathan S (2003) MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules. Bioinformatics 19(2):309–310PubMedCrossRefGoogle Scholar
  36. 36.
    Tong JC, Kong L, Tan TW, Ranganathan S (2006) MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions. Appl Bioinformatics 5(2):111–114PubMedCrossRefGoogle Scholar
  37. 37.
    Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14(6):1188–1190PubMedCentralPubMedCrossRefGoogle Scholar
  38. 38.
    Ehrenmann F, Kaas Q, Lefranc MP (2010) IMGT/3Dstructure-DB and IMGT/Domain GapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res 38 (Database issue):D301–D307PubMedCentralPubMedCrossRefGoogle Scholar
  39. 39.
    Ehrenmann F, Lefranc MP (2011) IMGT/ 3Dstructure-DB: querying the IMGT database for 3D structures in immunology and immunoinformatics (IG or antibodies, TR, MH, RPI, and FPIA). Cold Spring Harb Protoc 2011(6):750–761PubMedGoogle Scholar
  40. 40.
    Beaver JE, Bourne PE, Ponomarenko JV (2007) EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). Immunome Res 3:3PubMedCentralPubMedCrossRefGoogle Scholar
  41. 41.
    Sinigaglia M, Antunes DA, Rigo MM, Chies JA, Vieira GF (2013) CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes. Database, Oxford 2013:bat002Google Scholar
  42. 42.
    Antunes DA, Vieira GF, Rigo MM, Cibulski SP, Sinigaglia M, Chies JA (2010) Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment. PLoS One 5(4):e10353PubMedCentralPubMedCrossRefGoogle Scholar
  43. 43.
    Antunes DA, Rigo MM, Silva JP, Cibulski SP, Sinigaglia M, Chies JA, Vieira GF (2011) Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A*02:01 allele. Mol Immunol 48(12–13): 1461–1467PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.School of Pharmacy & Ph.D. Program in ToxicologyKaohsiung Medical UniversityKaohsiungTaiwan

Personalised recommendations