Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Research Article
  • Published:

Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices

Nature Biotechnology volume 17, pages 555–561 (1999)Cite this article

Abstract

Most pockets in the human leukocyte antigen–group DR (HLA-DR) groove are shaped by clusters of polymorphic residues and, thus, have distinct chemical and size characteristics in different HLA-DR alleles. Each HLA-DR pocket can be characterized by "pocket profiles," a quantitative representation of the interaction of all natural amino acid residues with a given pocket. In this report we demonstrate that pocket profiles are nearly independent of the remaining HLA-DR cleft. A small database of profiles was sufficient to generate a large number of HLA-DR matrices, representing the majority of human HLA-DR peptide-binding specificity. These virtual matrices were incorporated in software (TEPITOPE) capable of predicting promiscuous HLA class II ligands. This software, in combination with DNA microarray technology, has provided a new tool for the generation of comprehensive databases of candidate promiscuous T-cell epitopes in human disease tissues. First, DNA microarrays are used to reveal genes that are specifically expressed or upregulated in disease tissues. Second, the prediction software enables the scanning of these genes for promiscuous HLA-DR binding sites. In an example, we demonstrate that starting from nearly 20,000 genes, a database of candidate colon cancer–specific and promiscuous T-cell epitopes could be fully populated within a matter of days. Our approach has implications for the development of epitope-based vaccines.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Allele independence of pocket profiles leads to wide coverage of HLA-DR binding specificity.
Figure 2: Function of the TEPITOPE software.
Figure 3: Validation of TEPITOPE using large peptide repertoires.
Figure 4: Examples for tumor antigen identification by DNA microarray technology.

Similar content being viewed by others

References

  1. Germain, R.N. MHC-dependent antigen processing and peptide presentation: providing ligands for T lymphocyte activation. Cell 76, 287 –299 (1994).

    Article  CAS  Google Scholar 

  2. Topalian, S.L. MHC class II restricted tumor antigens and the role of CD4 T cells in cancer immunotherapy. Curr. Opin. Immunol. 6, 741 –745 (1994).

    Article  CAS  Google Scholar 

  3. Stern, L.J. et al. Crystal structure of the human class II MHC protein HLA-DR1 complexed with an Influenza virus peptide. Nature 368, 215–221 (1994).

    Article  CAS  Google Scholar 

  4. Brown, J.H. et al. The three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364, 33– 39 (1993).

    Article  CAS  Google Scholar 

  5. Ghosh, P., Amaya, M., Mellins, E. & Wiley, D.C. The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3. Nature 378, 457–462 ( 1995).

    Article  CAS  Google Scholar 

  6. Dessen, A., Lawrence, M.C., Cupo, S., Zaller, D.M. & Wiley, D.C. X-ray crystal structure of HLA-DR4 (DRA*0101, DRB1*0401) complexed with a peptide from human collagene II. Immunity 7, 473–481 (1997).

    Article  CAS  Google Scholar 

  7. Sinigaglia, F. & Hammer, J. Defining rules for the peptide-MHC class II interaction. Curr. Opin. Immunol. 6, 52–56 (1994).

    Article  CAS  Google Scholar 

  8. Hammer, J. et al. Precise prediction of major histocompatibility complex class II peptide interaction based on peptide side chain scanning. J. Exp. Med. 180, 2353–2358 (1994).

    Article  CAS  Google Scholar 

  9. Marshall, K.W. et al. Prediction of peptide affinity to HLA DRB1*0401. J. Immunol. 154, 5927–5933 ( 1995).

    CAS  PubMed  Google Scholar 

  10. Brusic, V., Rudy, G., Honeyman, G., Hammer, J. & Harrison, L. Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. Bioinformatics 14, 121–30 ( 1998).

    Article  CAS  Google Scholar 

  11. Sette, A. et al. Structural characteristics of an antigen required for its interaction with Ia and recognition by T cells. Nature 328, 395–399 (1987).

    Article  CAS  Google Scholar 

  12. Hammer, J., Sturniolo, T. & Sinigaglia, F. HLA class II peptide binding specificity and autoimmunity. Adv Immunol 66, 67-100 (1997).

    Article  CAS  Google Scholar 

  13. Hammer, J. & Sinigaglia, F. in MHC Vol. 2, Vol. 181 (eds Fernandez, N. & Butcher, G.) 197–228 (Oxford Univ. Press, New York, 1998).

    Google Scholar 

  14. Hammer, J. New methods to predict MHC-binding sequences within protein antigens. Curr. Opin. Immunol. 7, 263–269 (1995).

    Article  CAS  Google Scholar 

  15. Marsh, S.G.E. Nomenclature for factors of the HLA system, update January 1998. Tissue Antigens 51, 582–583 (1998).

    Article  CAS  Google Scholar 

  16. Lockhart, D.J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays [see comments]. Nat. Biotechnol. 14, 1675–1680 (1996).

    Article  CAS  Google Scholar 

  17. Wodicka, L., Dong, H., Mittmann, M., Ho, M.H. & Lockhart, D.J. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15, 1359– 1367 (1997).

    Article  CAS  Google Scholar 

  18. Gross, D.M. et al. Identification of LFA-1 as a candidate autoantigen in treatment-resistant Lyme arthritis. Science 281, 703– 706 (1998).

    Article  CAS  Google Scholar 

  19. Hammer, J. et al. Peptide binding specificity of HLA-DR4 molecules: correlation with rheumatoid arthritis association. J. Exp. Med. 181, 1847–1855 (1995).

    Article  CAS  Google Scholar 

  20. Tsuji, K., Aizawa, M. & Sasazuki, T. HLA 1991; Proceedings of the eleventh international histocompatibility workshop and conference (Oxford Univ. Press, New York, 1992).

    Google Scholar 

  21. Manici, S. et al. Melanoma cells present a MAGE-3 epitope to CD4(+) cytotoxic T cells in association with histocompatibility leukocyte antigen DR11. J. Exp. Med. 189, 871–876 (1999).

    Article  CAS  Google Scholar 

  22. Topalian, S.L. et al. Melanoma-specific CD4 T cells recognize nonmutated HLA-DR-restricted tyrosinase epitopes. J. Exp. Med. 183, 1965 –1971 (1996).

    Article  CAS  Google Scholar 

  23. Hammer, J., Takacs, B. & Sinigaglia, F. Identification of a motif for HLA-DR1 binding peptides using M13 display libraries. J. Exp. Med. 176, 1007–1013 (1992).

    Article  CAS  Google Scholar 

  24. Hammer, J. et al. Promiscuous and allele-specific anchors in HLA-DR binding peptides. Cell 74, 197–203 ( 1993).

    Article  CAS  Google Scholar 

  25. Rammensee, H.G., Bachmann, J., Emmerich, N. & Stevanovic, S. SYFPEITHI: an internet database for MHC ligands and peptide motifs (access via http://www.uni-tuebingen.de/uni/kxi/). (data extracted in 4Q, 1998).

  26. Blackwell, J.M. Parasite genome analysis. Progress in the Leishmania genome project. Trans. R. Soc. Trop. Med. Hyg. 91, 107– 110 (1997).

    Article  CAS  Google Scholar 

  27. Collins, F.S. et al. New goals for the U.S. Human Genome Project: 1998-2003. Science 282, 682–689 ( 1998).

    Article  CAS  Google Scholar 

  28. Harwood, C.R. & Wipat, A. Sequencing and functional analysis of the genome of Bacillus subtilis strain 168. FEBS Lett. 389, 84–87 (1996).

    Article  CAS  Google Scholar 

  29. Degrave, W., Levin, M.J., da Silveira, J.F. & Morel, C.M. Parasite genome projects and the Trypanosoma cruzi genome initiative. Mem. Inst. Oswaldo Cruz 92, 859–862 (1997).

    Article  CAS  Google Scholar 

  30. Adams, M.D. et al. Sequence identification of 2,375 human brain genes [see comments]. Nature 355, 632–634 (1992).

    Article  CAS  Google Scholar 

  31. Adams, M.D. et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651– 1656 (1991).

    Article  CAS  Google Scholar 

  32. Ossendorp, F., Mengede, E., Camps, M., Filius, R. & Melief, C.J. Specific T helper cell requirement for optimal induction of cytotoxic T lymphocytes against major histocompatibility complex class II negative tumors. J. Exp. Med. 187, 693 –702 (1998).

    Article  CAS  Google Scholar 

  33. Sahin, U., Türeci, Ö. & Pfreundschuh, M. Serological identification of human tumor antigens. Curr. Opin. Immunol. 9, 709–716 (1997).

    Article  CAS  Google Scholar 

  34. Raddrizzani, L. et al. Different modes of peptide interaction enable HLA-DQ and HLA-DR molecules to bind diverse peptide repertoires. J. Immunol. 159, 703–711 (1997).

    CAS  PubMed  Google Scholar 

  35. Panina-Bordignon, P. et al. Universally immunogenic T cell epitopes: promiscuous binding to human MHC class II and promiscuous recognition by T cells. Eur. J. Immunol. 19, 2237–2242 (1989).

    Article  CAS  Google Scholar 

  36. Ben-Mahrez, K., Thierry, D., Sorokine, I., Danna-Muller, A. & Kohiyama, M. Detection of circulating antibodies against c-myc protein in cancer patient sera. Br. J. Cancer 57, 529–534 (1988).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Roche Milano Ricerche, Milan, 20132, Italy

    Tiziana Sturniolo, Elisa Bono, Fabio Gallazzi, Francesco Sinigaglia & Juergen Hammer

  2. Department of Genomics and Information Sciences, Hoffman-La Roche, Nutley, 07110, NJ

    Jiayi Ding, Laura Raddrizzani, Michael Braxenthaler & Juergen Hammer

  3. Department of Internal Medicine, University of Saarland, Homburg, 66421, Germany

    Oezlem Tuereci & Ugur Sahin

  4. Laboratory of Tumor Immunology, Scientific Institute H. San Raffaele, Milan, 20132, Italy

    Maria Pia Protti

Authors
  1. Tiziana Sturniolo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Elisa Bono
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jiayi Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Laura Raddrizzani
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Oezlem Tuereci
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ugur Sahin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Michael Braxenthaler
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Fabio Gallazzi
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Maria Pia Protti
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Francesco Sinigaglia
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Juergen Hammer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Juergen Hammer.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sturniolo, T., Bono, E., Ding, J. et al. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol 17, 555–561 (1999). https://doi.org/10.1038/9858

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/9858

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing