NetCTLpan: Pan-specific MHC class I pathway epitope predictions

Immunogenetics

Volumn 62, Issue 6, 2010, Pages 357-368

  Stranzl, Thomas ^a   Larsen, Mette Voldby ^a   Lundegaard, Claus ^a   Nielsen, Morten ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

CTL epitope; HLA; MHC class I pathway; MHC polymorphism; Pan specific prediction

Indexed keywords

EPITOPE; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; PROTEASOME; TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 1; ABC TRANSPORTER; HLA ANTIGEN CLASS 1; TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING (TAP);

ALLELE; AMINO ACID SEQUENCE; AREA UNDER THE CURVE; ARTICLE; BINDING AFFINITY; COMPUTER PREDICTION; CONTROLLED STUDY; CYTOTOXIC T LYMPHOCYTE; HUMAN; PRIORITY JOURNAL; IMMUNOLOGY; METABOLISM; PHYSIOLOGY; PROTEIN TRANSPORT;

ATP-BINDING CASSETTE TRANSPORTERS; EPITOPES, T-LYMPHOCYTE; HISTOCOMPATIBILITY ANTIGENS CLASS I; HUMANS; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN TRANSPORT; T-LYMPHOCYTES, CYTOTOXIC;

EID: 77953149616     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-010-0441-4     Document Type: Article

References (40)

1. Y Altuvia H Margalit 2000 Sequence signals for generation of antigenic peptides by the proteasome: implications for proteasomal cleavage mechanism J Mol Biol 295 879 890 10.1006/jmbi.1999.3392 1:CAS:528:DC%2BD3cXot12rtw%3D%3D 10656797
2. KS Anderson J Alexander M Wei P Cresswell 1993 Intracellular transport of class I MHC molecules in antigen processing mutant cell lines J Immunol 151 3407 3419 1:CAS:528:DyaK2cXivVyksg%3D%3D 8376783
3. V Brusic P van Endert J Zeleznikow S Daniel J Hammer N Petrovsky 1999 A neural network model approach to the study of human TAP transporter In Silico Biol 1 109 121 1:CAS:528:DyaK1MXms1Srt7s%3D 11471244
4. A Craiu T Akopian A Goldberg KL Rock 1997 Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide Proc Natl Acad Sci USA 94 10850 10855 10.1073/pnas.94.20. 10850 1:CAS:528:DyaK2sXmtlChtLk%3D 9380723 (Pubitemid 27430824)
5. I Doytchinova P Guan D Flower 2006 EpiJen: a server for multistep T cell epitope prediction BMC Bioinformatics 7 131 10.1186/1471-2105-7-131 16533401
6. P Dönnes O Kohlbacher 2005 Integrated modeling of the major events in the MHC class I antigen processing pathway Protein Sci 14 2132 2140 10.1110/ps.051352405 15987883 (Pubitemid 41132379)
7. J Hakenberg A Nussbaum H Schild H Rammensee C Kuttler H Holzhütter P Kloetzel S Kaufmann H Mollenkopf 2003 MAPPP: MHC class I antigenic peptide processing prediction Appl Bioinformatics 2 155 158 1:CAS:528: DC%2BD2cXotlartg%3D%3D 15130801
8. RA Henderson H Michel K Sakaguchi J Shabanowitz E Appella DF Hunt VH Engelhard 1992 HLA-A2.1-associated peptides from a mutant cell line: a second pathway of antigen presentation Science 255 1264 1266 10.1126/science.1546329 1:CAS:528:DyaK38XhslWrsLg%3D 1546329
9. I Hoof B Peters J Sidney LE Pedersen A Sette O Lund S Buus M Nielsen 2009 NetMHCpan, a method for MHC class I binding prediction beyond humans Immunogenetics 61 1 13 10.1007/s00251-008-0341-z 1:CAS:528:DC%2BD1MXhtlKltbw%3D 19002680
10. AS Juncker MV Larsen N Weinhold M Nielsen S Brunak O Lund 2009 Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands PLoS ONE 4 e7448 10.1371/journal.pone.0007448 19826487
11. J Koch R Guntrum S Heintke C Kyritsis R Tampé 2004 Functional dissection of the transmembrane domains of the transporter associated with antigen processing (TAP) J Biol Chem 279 10142 10147 10.1074/jbc.M312816200 1:CAS:528:DC%2BD2cXhvFCitbg%3D 14679198 (Pubitemid 38372619)
12. MV Larsen C Lundegaard K Lamberth S Buus S Brunak O Lund M Nielsen 2005 An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions Eur J Immunol 35 2295 2303 10.1002/eji.200425811 1:CAS:528:DC%2BD2MXps1GmtL0%3D 15997466 (Pubitemid 41179750)
13. MV Larsen C Lundegaard K Lamberth S Buus O Lund M Nielsen 2007 Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction BMC Bioinformatics 8 424 10.1186/1471-2105-8-424 17973982
14. F Lévy L Burri S Morel A Peitrequin N Lévy A Bachi U Hellman BJ Van Den Eynde C Servis 2002 The final N-terminal trimming of a subaminoterminal proline-containing HLA class I-restricted antigenic peptide in the cytosol is mediated by two peptidases J Immunol 169 4161 4171 12370345
15. O Lund M Nielsen C Kesmir AG Petersen C Lundegaard P Worning C Sylvester-Hvid K Lamberth G Røder S Justesen S Buus S Brunak 2004 Definition of supertypes for HLA molecules using clustering of specificity matrices Immunogenetics 55 797 810 10.1007/s00251-004-0647-4 1:CAS:528:DC%2BD2cXisV2isLg%3D 14963618 (Pubitemid 38650985)
16. Lund O, Nielsen M, Lundegaard C, Kesmir C, Brunak S (2005) Immunological bioinformatics, 1 ed. MIT press
17. C Lundegaard O Lund M Nielsen 2008 Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers Bioinformatics 24 1397 1398 10.1093/bioinformatics/btn128 1:CAS:528:DC%2BD1cXmtVaisL0%3D 18413329 (Pubitemid 351737147)
18. A MacNamara U Kadolsky CR Bangham B Asquith 2009 T-cell epitope prediction: rescaling can mask biological variation between MHC molecules PLoS Comput Biol 5 e1000327 10.1371/journal.pcbi.1000327 19300484
19. XY Mo P Cascio K Lemerise AL Goldberg K Rock 1999 Distinct proteolytic processes generate the C and N termini of MHC class I-binding peptides J Immunol 163 5851 5859 1:CAS:528:DyaK1MXns12rs7w%3D 10570269
20. M Nielsen C Lundegaard O Lund C Keşmir 2005 The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage Immunogenetics 57 33 41 10.1007/s00251-005-0781-7 1:CAS:528:DC%2BD2MXjtlartbg%3D 15744535 (Pubitemid 40591245)
21. M Nielsen C Lundegaard T Blicher K Lamberth M Harndahl S Justesen G Røder B Peters A Sette O Lund S Buus 2007 NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence PLoS ONE 2 e796 10.1371/journal.pone.0000796 17726526 (Pubitemid 351386580)
22. P Paz N Brouwenstijn R Perry N Shastri 1999 Discrete proteolytic intermediates in the MHC class I antigen processing pathway and MHC I-dependent peptide trimming in the ER Immunity 11 241 251 10.1016/S1074-7613(00)80099-0 1:CAS:528:DyaK1MXlvVSgtLo%3D 10485659 (Pubitemid 29428817)
23. CL Pérez MV Larsen R Gustafsson MM Norström A Atlas DF Nixon M Nielsen O Lund AC Karlsson 2008 Broadly immunogenic HLA class I supertype-restricted elite CTL epitopes recognized in a diverse population infected with different HIV-1 subtypes J Immunol 180 5092 5100 18354235
24. B Peters S Bulik R Tampe PM Van Endert H Holzhütter 2003 Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors J Immunol 171 1741 1749 1:CAS:528:DC%2BD3sXmtVWntrY%3D 12902473
25. H Rammensee J Bachmann NP Emmerich Oa Bachor S Stevanović 1999 SYFPEITHI: database for MHC ligands and peptide motifs Immunogenetics 50 213 219 10.1007/s002510050595 1:CAS:528:DyaK1MXntlalsbs%3D 10602881
26. X Rao AI Costa D van Baarle C Kesmir 2009 A comparative study of HLA binding affinity and ligand diversity: implications for generating immunodominant CD8+ T cell responses J Immunol 182 1526 1532 1:CAS:528:DC%2BD1MXnsVeruw%3D%3D 19155500
27. U Ritz B Seliger 2001 The transporter associated with antigen processing (TAP): structural integrity, expression, function, and its clinical relevance Mol Med 7 149 158 1:CAS:528:DC%2BD3MXjtFWntrw%3D 11471551
28. MM Schatz B Peters N Akkad N Ullrich AN Martinez O Carroll S Bulik H Rammensee P van Endert H Holzhütter S Tenzer H Schild 2008 Characterizing the N-terminal processing motif of MHC class I ligands J Immunol 180 3210 3217 1:CAS:528:DC%2BD1cXit1OksLs%3D 18292545
29. J Sidney B Peters N Frahm C Brander A Sette 2008 HLA class I supertypes: a revised and updated classification BMC Immunology 9 1 10.1186/1471-2172-9-1 18211710 (Pubitemid 351283143)
30. KD Smith CT Lutz 1996 Peptide-dependent expression of HLA-B7 on antigen processing-deficient T2 cells J Immunol 156 3755 3764 1:CAS:528: DyaK28XivVamsrg%3D 8621911
31. L Stoltze TP Dick M Deeg B Pömmerl HG Rammensee H Schild 1998 Generation of the vesicular stomatitis virus nucleoprotein cytotoxic T lymphocyte epitope requires proteasome-dependent and -independent proteolytic activities Eur J Immunol 28 4029 4036 10.1002/(SICI)1521-4141(199812)28: 12<4029::AID-IMMU4029>3.0.CO;2-N 1:CAS:528:DyaK1cXotVSmsbs%3D 9862339
32. T Sturniolo E Bono J Ding L Raddrizzani O Tuereci U Sahin M Braxenthaler F Gallazzi MP Protti F Sinigaglia J Hammer 1999 Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices Nat Biotechnol 17 555 561 10.1038/9858 1:CAS:528:DyaK1MXjs1Kgu7k%3D 10385319 (Pubitemid 29262918)
33. ST Tang M Wang K Lamberth M Harndahl MH Dziegiel MH Claesson S Buus O Lund 2008 MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination Arch Virol 153 1833 1844 10.1007/s00705-008-0194-7 1:CAS:528:DC%2BD1cXht1eitL3P 18797815
34. S Tenzer B Peters S Bulik O Schoor C Lemmel MM Schatz P Kloetzel H Rammensee H Schild H Holzhütter 2005 Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding Cell Mol Life Sci: CMLS 62 1025 1037 10.1007/s00018-005-4528-2 1:CAS:528:DC%2BD2MXkslOlsLs%3D 15868101 (Pubitemid 40655618)
35. Uniprot consortium 2009 The universal protein resource (UniProt) 2009 Nucleic Acids Res 37 169 174 10.1093/nar/gkn664
36. M Wang K Lamberth M Harndahl G Røder A Stryhn MV Larsen M Nielsen C Lundegaard ST Tang MH Dziegiel J Rosenkvist AE Pedersen S Buus MH Claesson O Lund 2007 CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening Vaccine 25 2823 2831 10.1016/j.vaccine.2006. 12.038 1:CAS:528:DC%2BD2sXjtFGqtrk%3D 17254671 (Pubitemid 46420615)
37. EJ Wherry TN Golovina SE Morrison G Sinnathamby MJ McElhaugh DC Shockey LC Eisenlohr 2006 Re-evaluating the generation of a "proteasome- independent" MHC class I-restricted CD8 T cell epitope J Immunol 61 2249
38. JW Yewdell JR Bennink 1999 Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses Annu Rev Immunol 17 51 88 10.1146/annurev.immunol.17.1.51 1:CAS:528:DyaK1MXjtVSrsbk%3D 10358753 (Pubitemid 29241119)
39. PM van Endert R Tampé TH Meyer R Tisch JF Bach HO McDevitt 1994 A sequential model for peptide binding and transport by the transporters associated with antigen processing Immunity 1 491 500 10.1016/1074-7613(94) 90091-4 7895159 (Pubitemid 2142273)
40. H Zhang C Lundegaard M Nielsen 2009 Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods Bioinformatics 25 83 89 10.1093/bioinformatics/btn579 18996943