Human self-protein CD8+ T-cell epitopes are both positively and negatively selected

European Journal of Immunology

Volumn 39, Issue 4, 2009, Pages 1056-1065

  Almani, Michal ^a   Raffaeli, Shai ^a   Vider Shalit, Tal ^a   Tsaban, Lea ^a   Fishbain, Vered ^b   Louzoun, Yoram ^a  

^a BAR ILAN UNIVERSITY   (Israel)

^b HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

Autoimmunity; Bioinformatics; CD8 T cells; Self non self discrimination

Indexed keywords

AUTOIMMUNE REGULATOR PROTEIN; EPITOPE; HLA ANTIGEN; AUTOANTIGEN; HISTOCOMPATIBILITY ANTIGEN;

ALLELE; AMINO ACID SEQUENCE; ANTIGEN PRESENTATION; ARTICLE; AUTOIMMUNITY; CD8+ T LYMPHOCYTE; CELL SELECTION; CELLULAR IMMUNITY; CONTROLLED STUDY; HUMAN; HUMAN CELL; INNATE IMMUNITY; PRIORITY JOURNAL; PROTEIN EXPRESSION; SINGLE NUCLEOTIDE POLYMORPHISM; T LYMPHOCYTE; UPREGULATION; BIOLOGY; GENE FREQUENCY; GENETICS; HUMAN GENOME; IMMUNOLOGY;

ALLELES; AUTOANTIGENS; CD8-POSITIVE T-LYMPHOCYTES; COMPUTATIONAL BIOLOGY; EPITOPES, T-LYMPHOCYTE; GENE FREQUENCY; GENOME, HUMAN; HISTOCOMPATIBILITY ANTIGENS; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 65449165731     PISSN: 00142980     EISSN: 15214141     Source Type: Journal    
DOI: 10.1002/eji.200838353     Document Type: Article

References (46)

1. Hozumi, N. and Tonegawa, S., Evidence for somatic rearrangement of immunoglobulin genes coding for variable and constant regions. Proc. Natl. Acad. Sci. USA 1976. 73: 3628-3632.
2. Early, P., Huang, H., Davis, M., Calame, K. and Hood, L., An immunoglobulin heavy chain variable region gene is generated from three segments of DNA: VH, D and JH. Cell 1980. 19: 981-992.
3. Weigert, M., Perry, R., Kelley, D., Hunkapiller, T., Schilling, J. and Hood, L., The joining of V and J gene segments creates antibody diversity. Nature 1980. 283: 497-499.
4. Nemazee, D., Russell, D., Arnold, B., Haemmerling, G., Allison, J., Miller, J. F., Morahan, G. and Buerki, K., Clonal deletion of autospecific B lymphocytes. Immunol. Rev. 1991. 122: 117-132.
5. Prak, E. L. and Weigert, M., Light chain replacement: A new model for antibody gene rearrangement. J. Exp. Med. 1995. 182: 541-548.
6. Miller, J. F., Self-nonself discrimination and tolerance in T and B lymphocytes. Immunol. Res. 1993. 12: 115-130.
7. Cope, A. P., Schulze-Koops, H. and Aringer, M., The central role of T cells in rheumatoid arthritis. Clin. Exp. Rheumatol. 2007. 25: S4-S11.
8. Wilczynski, J. R., Kalinka, J. and Radwan, M., The role of T-regulatory cells in pregnancy and cancer. Front. Biosci. 2008. 13: 2275-2289.
9. Williams, A., Peh, C. A. and Elliott, T., The cell biology of MHC class I antigen presentation. Tissue Antigens 2002. 59: 3-17.
10. Rock, K. L., York, I. A., Saric, T. and Goldberg, A. L., Protein degradation and the generation of MHC class I-presented peptides. Adv. Immunol. 2002. 80: 1-70.
11. Uebel, S. and Tampe, R., Specificity of the proteasome and the TAP transporter. Curr. Opin. Immunol. 1999. 11: 203-208.
12. Rammensee, H. G., Bachmann, J. and Stevanović, S. S., MHC Ligands and Peptide Motifs, Austin Texas, USA 1997.
13. Parker, K. C., Bednarek, M. A., Hull, L. K., Utz, U., Cunningham, B., Zweerink, H. J., Biddison, W. E. and Coligan, J. E., Sequence motifs important for peptide binding to the human MHC class I molecule, HLA-A2. J. Immunol. 1992. 149: 3580-3587.
14. Buus, S., Lauemoller, S. L., Worning, P., Kesmir, C., Frimurer, T., Corbet, S., Fomsgaard, A. et al., Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens 2003. 62: 378-384.
15. Bui, H. H., Sidney, J., Peters, B., Sathiamurthy, M., Sinichi, A., Purton, K. A., Mothe, B. R. et al., Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 2005. 57: 304-314.
16. Bhasin, M. and Raghava, G. P., Pcleavage: An SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences. Nucleic Acids Res. 2005. 33: W202-W207.
17. Saxova, P., Buus, S., Brunak, S. and Kesmir, C., Predicting proteasomal cleavage sites: A comparison of available methods. Int. Immunol. 2003. 15: 781-787.
18. Kesmir, C., Nussbaum, A. K., Schild, H., Detours, V. and Brunak, S., Prediction of proteasome cleavage motifs by neural networks. Protein Eng. 2002. 15: 287-296.
19. Nielsen, M., Lundegaard, C., Lund, O. and Kesmir, C., The role of the proteasome in generating cytotoxic T-cell epitopes: Insights obtained from improved predictions of proteasomal cleavage. Immunogenetics 2005. 57: 33-41.
20. Singh, H. and Raghava, G. P., ProPred: Prediction of HLA-DR binding sites. Bioinformatics 2001. 17: 1236-1237.
21. Louzoun, Y., Vider, T. and Weigert, M., T-cell epitope repertoire as predicted from human and viral genomes. Mol. Immunol. 2006. 43: 559-569.
22. Birney, E., Andrews, T. D., Bevan, P., Caccamo, M., Chen, Y., Clarke, L., Coates, G. et al., An overview of ensembl, Ensembl 2004. Genome Res. 2004. 14: 925-928.
23. Louzoun, Y. and Vider, T., Score for proteasomal peptide production probability. Immunology 2004. 1.
24. Ginodi, I., Vider-Shalit, T., Tsaban, L. and Louzoun, Y., Precise score for the prediction of peptides cleaved by the proteasome. Bioinformatics 2008. 24: 477-483.
25. Peters, B., Bulik, S., Tampe, R., Endert, P. M. V. and Holzhutter, H. G., Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J. Immunol. 2003. 171: 1741-1749.
26. Parham, P. and Ohta, T., Population biology of antigen presentation by MHC class I molecules. Science 1996. 272: 67-74.
27. Sathiamurthy, M., Hickman, H. D., Cavett, J.W., Zahoor, A., Prilliman, K., Metcalf, S., Fernandez Vina, M. and Hildebrand, W. H., Population of the HLA ligand database. Tissue Antigens 2003. 61: 12-19.
28. Vider-Shalit, T., Fishbain, V., Raffaeli, S. and Louzoun, Y., Phase dependent immune evasion of Herpesviruses. J. Virol. 2007. 81: 9536-9545.
29. Gotter, J., Brors, B., Hergenhahn, M. and Kyewski, B., Medullary epithelial cells of the human thymus express a highly diverse selection of tissue-specific genes colocalized in chromosomal clusters. J. Exp. Med. 2004. 199: 155-166.
30. Kont, V., Laan, M., Kisand, K., Merits, A., Scott, H. S. and Peterson, P., Modulation of Aire regulates the expression of tissue-restricted antigens. Mol. Immunol. 2007. 45: 25-33.
31. Sillanpaa, N., Magureanu, C. G., Murumagi, A., Reinikainen, A., West, A., Manninen, A., Lahti, M. et al., Autoimmune regulator induced changes in the gene expression profile of human monocyte-dendritic cell-lineage. Mol. Immunol. 2004. 41: 1185-1198.
32. + T cells by DNA vaccination depends on appropriate targeting of sufficient levels of immunologically relevant antigen to appropriate processing pathways. J. Immunol. 2002. 169: 4951-4960.
33. Rebhan, M., Chalifa-Caspi, V., Prilusky, J. and Lancet, D., GeneCards: Encyclopedia for Genes, Proteins and Diseases, Weizmann Institute of Science, Bioinformatics Unit and Genome Center, Rehovot, Israel 1997.
34. Dhodapkar, M. V. and Steinman, R. M., Antigen-bearing immature dendritic cells induce peptide-specific CD8(+) regulatory T cells in vivo in humans. Blood 2002. 100: 174-177.
35. Brusic, V., Rudy, G. and Harrison, L. C., MHCPEP, a database of MHC-binding peptides: Update 1997. Nucleic Acids Res. 1998. 26: 368-371.
36. Rammensee, H., Bachmann, J., Emmerich, N. P., Bachor, O. A. and Stevanovic, S., SYFPEITHI: Database for MHC ligands and peptide motifs. Immunogenetics 1999. 50: 213-219.
37. Kirkpatrick, S., Gelatt, C. D. and Vecchi, M. P., Optimization by Simulated Annealing. Science 1983. 220: 671-680.
38. Robinson, J., Waller, M. J., Parham, P., Bodmer, J. G. and Marsh, S. G. E., IMGT/HLA Database - a sequence database for the human major histocompatibility complex. Nucleic Acids Res. 2001. 29: 210-213.
39. Marsh, S. G. E., Parham, P. and Barber, L. D., The HLA Facts Book. Academic Press, London, UK 2000.
40. Peters, B., Sidney, J., Bourne, P., Bui, H. H., Buus, S., Doh, G., Fleri, W. et al., The immune epitope database and analysis resource: From vision to blueprint. PLoS Biol. 2005. 3: e91.
41. Sathiamurthy, M., Peters, B.,Bui,H.H., Sidney, J., Mokili, J., Wilson, S. S., Fleri, W. et al., An ontology for immune epitopes: Application to the design of a broad scope database of immune reactivities. Immunome Res. 2005. 1: 2.
42. Bhasin, M., Singh, H. and Raghava, G. P., MHCBN: A comprehensive database of MHC binding and non-binding peptides. Bioinformatics 2003. 19: 665-666.
43. Govindarajan, K. R., Kangueane, P., Tan, T. W. and Ranganathan, S., MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules. Bioinformatics 2003. 19: 309-310.
44. Chalifa-Caspi, V., Shmueli, O., Benjamin-Rodrig, H., Rosen, N., Shmoish, M., Yanai, I., Ophir, R. et al., GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia. Brief Bioinform. 2003. 4: 349-360.
45. Shmueli, O., Horn-Saban, S., Chalifa-Caspi, V., Shmoish, M., Ophir, R., Benjamin-Rodrig, H., Safran, M. et al., GeneNote: Whole genome expression profiles in normal human tissues. C. R. Biol. 2003. 326: 1067-1072.
46. Yanai, I., Benjamin, H., Shmoish, M., Chalifa-Caspi, V., Shklar, M., Ophir, R., Bar-Even, A. et al., Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 2005. 21: 650-659.