Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction

Mette Voldby Larsen1, Claus Lundegaard1, Kasper Lamberth2, Søren Buus2, Ole Lund1, Morten Nielsen1
1Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Building 208, DK-2800, Lyngby, Denmark
2Institute for Medical Microbiology and Immunology, Panum Institute 18.3.12, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark

Tóm tắt

Từ khóa


Tài liệu tham khảo

Stoltze L, Dick TP, Deeg M, Pommerl B, Rammensee HG, Schild H: Generation of the vesicular stomatitis virus nucleoprotein cytotoxic T lymphocyte epitope requires proteasome-dependent and -independent proteolytic activities. Eur J Immunol 1998, 28(12):4029–4036. 10.1002/(SICI)1521-4141(199812)28:12<4029::AID-IMMU4029>3.0.CO;2-N

Mo XY, Cascio P, Lemerise K, Goldberg AL, Rock K: Distinct proteolytic processes generate the C and N termini of MHC class I-binding peptides. J Immunol 1999, 163(11):5851–5859.

Altuvia Y, Margalit H: Sequence signals for generation of antigenic peptides by the proteasome: implications for proteasomal cleavage mechanism. J Mol Biol 2000, 295(4):879–890. 10.1006/jmbi.1999.3392

Craiu A, Akopian T, Goldberg A, Rock KL: Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide. Proc Natl Acad Sci U S A 1997, 94(20):10850–10855. 10.1073/pnas.94.20.10850

Paz P, Brouwenstijn N, Perry R, Shastri N: Discrete proteolytic intermediates in the MHC class I antigen processing pathway and MHC I-dependent peptide trimming in the ER. Immunity 1999, 11(2):241–251. 10.1016/S1074-7613(00)80099-0

Ritz U, Seliger B: The transporter associated with antigen processing (TAP): structural integrity, expression, function, and its clinical relevance. Mol Med 2001, 7(3):149–158.

Koch J, Guntrum R, Heintke S, Kyritsis C, Tampe R: Functional dissection of the transmembrane domains of the transporter associated with antigen processing (TAP). J Biol Chem 2004, 279(11):10142–10147. 10.1074/jbc.M312816200

van Endert PM, Tampe R, Meyer TH, Tisch R, Bach JF, McDevitt HO: A sequential model for peptide binding and transport by the transporters associated with antigen processing. Immunity 1994, 1(6):491–500. 10.1016/1074-7613(94)90091-4

Yewdell JW, Bennink JR: Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu Rev Immunol 1999, 17: 51–88. 10.1146/annurev.immunol.17.1.51

Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M: 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 2005, 35(8):2295–2303. 10.1002/eji.200425811

SYFPEITHI Epitope Prediction[ http://www.syfpeithi.de/Scripts/MHCServer.dll/EpitopePrediction.htm ]

Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S: SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 1999, 50(3–4):213–219. 10.1007/s002510050595

BIMAS HLA Peptide Binding Prediction[ http://bimas.dcrt.nih.gov/molbio/hla_bind/ ]

Parker KC, Bednarek MA, Coligan JE: Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol 1994, 152(1):163–175.

Hakenberg J, Nussbaum AK, Schild H, Rammensee HG, Kuttler C, Holzhutter HG, Kloetzel PM, Kaufmann SH, Mollenkopf HJ: MAPPP: MHC class I antigenic peptide processing prediction. Appl Bioinformatics 2003, 2(3):155–158.

Doytchinova IA, Guan P, Flower DR: EpiJen: a server for multistep T cell epitope prediction. BMC Bioinformatics 2006, 7: 131. 10.1186/1471-2105-7-131

Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild H, Holzhutter HG: Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell Mol Life Sci 2005, 62(9):1025–1037. 10.1007/s00018-005-4528-2

Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C, Kostem E, Basch D, Lamberth K, Harndahl M, Fleri W, Wilson SS, Sidney J, Lund O, Buus S, Sette A: A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol 2006, 2(6):e65. 10.1371/journal.pcbi.0020065

Donnes P, Kohlbacher O: Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Sci 2005, 14(8):2132–2140. 10.1110/ps.051352405

Lund O, Nielsen M, Kesmir C, Petersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Roder G, Justesen S, Buus S, Brunak S: Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics 2004, 55(12):797–810. 10.1007/s00251-004-0647-4

Supplementary material for NetCTL-1.2[ http://www.cbs.dtu.dk/suppl/immunology/CTL-1.2.php ]

Tong JC, Tan TW, Ranganathan S: Methods and protocols for prediction of immunogenic epitopes. Brief Bioinform 2006.

Peters B, Bulik S, Tampe R, Van Endert PM, Holzhutter HG: Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol 2003, 171(4):1741–1749.

Larsen MV, Nielsen M, Weinzierl A, Lund O: TAP-Independent MHC Class I Presentation. Current Immunological Reviews 2006, 2: 233–245. 10.2174/157339506778018550

Henderson RA, Michel H, Sakaguchi K, Shabanowitz J, Appella E, Hunt DF, Engelhard VH: HLA-A2.1-associated peptides from a mutant cell line: a second pathway of antigen presentation. Science 1992, 255(5049):1264–1266. 10.1126/science.1546329

Smith KD, Lutz CT: Peptide-dependent expression of HLA-B7 on antigen processing-deficient T2 cells. J Immunol 1996, 156(10):3755–3764.

Wei ML, Cresswell P: HLA-A2 molecules in an antigen-processing mutant cell contain signal sequence-derived peptides. Nature 1992, 356(6368):443–446. 10.1038/356443a0

SYFPEITHI database[ http://www.syfpeithi.de ]

HIV Immunology CTL Database[ http://www.hiv.lanl.gov ]

Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S: Prediction of proteasome cleavage motifs by neural networks. Protein Eng 2002, 15(4):287–296. 10.1093/protein/15.4.287

Nielsen M, Lundegaard C, Lund O, Kesmir C: The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics 2005, 57(1–2):33–41. 10.1007/s00251-005-0781-7

Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, Buus S, Brunak S, Lund O: Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci 2003, 12(5):1007–1017. 10.1110/ps.0239403

NetMHC-3.0[ http://www.cbs.dtu.dk/services/NetMHC-3.0 ]

NetCTL[ http://www.cbs.dtu.dk/services/NetCTL ]

EpiJen[ http://www.jenner.ac.uk/EpiJen ]

MHC-I Antigenic Peptide Processing Prediction - MAPPP[ http://www.mpiib-berlin.mpg.de/MAPPP/ ]

Holzhutter HG, Frommel C, Kloetzel PM: A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20 S proteasome. J Mol Biol 1999, 286(4):1251–1265. 10.1006/jmbi.1998.2530

Holzhutter HG, Kloetzel PM: A kinetic model of vertebrate 20S proteasome accounting for the generation of major proteolytic fragments from oligomeric peptide substrates. Biophys J 2000, 79(3):1196–1205.

Kuttler C, Nussbaum AK, Dick TP, Rammensee HG, Schild H, Hadeler KP: An algorithm for the prediction of proteasomal cleavages. J Mol Biol 2000, 298(3):417–429. 10.1006/jmbi.2000.3683

Nussbaum AK, Kuttler C, Hadeler KP, Rammensee HG, Schild H: PAProC: a prediction algorithm for proteasomal cleavages available on the WWW. Immunogenetics 2001, 53(2):87–94. 10.1007/s002510100300

MHC pathway[ http://www.mhc-pathway.net ]

IEDB[ http://tools-int-01.liai.org/analyze/html/mhc_processing.html ]

WAPP[ http://www-bs.informatik.uni-tuebingen.de/WAPP ]

Armitage P, Berry G, Matthews JNS: Statistical Methods in Medical Research. 4th edition. Blackwell Science Ltd; 2002.